3-125929513-T-C

Variant names:

• chr3-125929513-T-C
• rs3828357
• ENST00000340333.8:n.711A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000340333.8(ENSG00000291096):​n.711A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.358 in 1,596,110 control chromosomes in the GnomAD database, including 104,343 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.33 (8870 hom., cov: 32)
  • Exomes 𝑓: 0.36 (95473 hom.)
• Consequence: ENSG00000291096 ENST00000340333.8 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.93
• Publications: 18 publications found

Genes affected

ENSG00000291096 (HGNC:):

ALG1L1P (HGNC:33721): (ALG1 like 1, pseudogene) Predicted to enable mannosyltransferase activity. Predicted to be involved in protein glycosylation. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

FAM86JP (HGNC:44097): (family with sequence similarity 86 member J, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.013293445).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000340333.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM86JP	NR_024250.1		n.1432T>C		non_coding_transcript_exon	Exon 5 of 5
	FAM86JP	NR_024251.1		n.1530T>C		non_coding_transcript_exon	Exon 5 of 5
	ALG1L1P	NR_171194.1		n.818A>G		non_coding_transcript_exon	Exon 7 of 7

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291096	ENST00000340333.8	TSL:1	n.711A>G		non_coding_transcript_exon	Exon 6 of 6
	FAM86JP	ENST00000467239.6	TSL:1	n.1484T>C		non_coding_transcript_exon	Exon 5 of 5
	FAM86JP	ENST00000485843.4	TSL:1	n.1654T>C		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50864 AN: 151892 Hom.: 8873 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.335

GnomAD2 exomes AF: 0.336 AC: 78478 AN: 233450 AF XY: 0.341

Gnomad AFR exome AF: 0.262

Gnomad AMR exome AF: 0.234

Gnomad ASJ exome AF: 0.448

Gnomad EAS exome AF: 0.280

Gnomad FIN exome AF: 0.429

Gnomad NFE exome AF: 0.382

Gnomad OTH exome AF: 0.357

GnomAD4 exome AF: 0.360 AC: 520248 AN: 1444100 Hom.: 95473 Cov.: 73 AF XY: 0.360 AC XY: 258706 AN XY: 718794

African (AFR) AF: 0.258 AC: 8628 AN: 33402

American (AMR) AF: 0.243 AC: 10854 AN: 44708

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 11788 AN: 26132

East Asian (EAS) AF: 0.277 AC: 11015 AN: 39694

South Asian (SAS) AF: 0.280 AC: 24126 AN: 86164

European-Finnish (FIN) AF: 0.418 AC: 15885 AN: 38032

Middle Eastern (MID) AF: 0.393 AC: 1624 AN: 4134

European-Non Finnish (NFE) AF: 0.373 AC: 415172 AN: 1111726

Other (OTH) AF: 0.352 AC: 21156 AN: 60108

GnomAD4 genome AF: 0.335 AC: 50862 AN: 152010 Hom.: 8870 Cov.: 32 AF XY: 0.333 AC XY: 24723 AN XY: 74276

African (AFR) AF: 0.264 AC: 10946 AN: 41482

American (AMR) AF: 0.274 AC: 4186 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1558 AN: 3464

East Asian (EAS) AF: 0.275 AC: 1421 AN: 5162

South Asian (SAS) AF: 0.276 AC: 1329 AN: 4810

European-Finnish (FIN) AF: 0.436 AC: 4598 AN: 10538

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25703 AN: 67944

Other (OTH) AF: 0.334 AC: 705 AN: 2112

Alfa AF: 0.360 Hom.: 3625

Bravo AF: 0.321

TwinsUK AF: 0.385 AC: 1426

ALSPAC AF: 0.369 AC: 1421

ESP6500AA AF: 0.269 AC: 737

ESP6500EA AF: 0.361 AC: 1670

ExAC AF: 0.338 AC: 38777

Asia WGS AF: 0.263 AC: 915 AN: 3478

EpiCase AF: 0.379

EpiControl AF: 0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Benign	-0.63	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	14
DANN	Benign	0.96
DEOGEN2	Benign	0.050	T
Eigen	Benign	-0.38
Eigen_PC	Benign	-0.43
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.75	T
MetaRNN	Benign	0.013	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.7	L
PhyloP100		4.9
PrimateAI	Uncertain	0.74	T
PROVEAN	Uncertain	-2.9	D
REVEL	Benign	0.18
Sift	Benign	0.081	T
Sift4G	Uncertain	0.053	T
Polyphen		0.59	P
Vest4		0.14
MPC		0.0062
ClinPred		0.036	T
GERP RS		2.3
Varity_R		0.25
gMVP		0.57
Mutation Taster		=85/15	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3828357; hg19: chr3-125648356; COSMIC: COSV61076292; COSMIC: COSV61076292;