rs3824830

Variant names:

• chr10-119081149-A-G
• rs3824830
• ENST00000687829.3:n.256A>G

Variant summary

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

The ENST00000687829.3(ENSG00000289126):​n.256A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 985,192 control chromosomes in the GnomAD database, including 81,559 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 0.32 (8755 hom., cov: 33)
  • Exomes 𝑓: 0.42 (72804 hom.)
• Consequence: ENSG00000289126 ENST00000687829.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 15 publications found

Genes affected

ENSG00000289126 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289126	ENST00000687829.3	n.256A>G		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49279 AN: 151964 Hom.: 8754 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.307

GnomAD4 exome AF: 0.415 AC: 345783 AN: 833110 Hom.: 72804 Cov.: 31 AF XY: 0.415 AC XY: 159848 AN XY: 384714

African (AFR) AF: 0.162 AC: 2563 AN: 15786

American (AMR) AF: 0.350 AC: 344 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1621 AN: 5152

East Asian (EAS) AF: 0.417 AC: 1514 AN: 3630

South Asian (SAS) AF: 0.309 AC: 5093 AN: 16460

European-Finnish (FIN) AF: 0.417 AC: 115 AN: 276

Middle Eastern (MID) AF: 0.273 AC: 443 AN: 1620

European-Non Finnish (NFE) AF: 0.425 AC: 323660 AN: 761904

Other (OTH) AF: 0.382 AC: 10430 AN: 27298

GnomAD4 genome AF: 0.324 AC: 49291 AN: 152082 Hom.: 8755 Cov.: 33 AF XY: 0.323 AC XY: 23990 AN XY: 74352

African (AFR) AF: 0.178 AC: 7381 AN: 41490

American (AMR) AF: 0.327 AC: 4995 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1132 AN: 3466

East Asian (EAS) AF: 0.391 AC: 2024 AN: 5176

South Asian (SAS) AF: 0.310 AC: 1497 AN: 4828

European-Finnish (FIN) AF: 0.377 AC: 3985 AN: 10562

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27315 AN: 67958

Other (OTH) AF: 0.307 AC: 647 AN: 2106

Alfa AF: 0.357 Hom.: 1960

Bravo AF: 0.317

Asia WGS AF: 0.317 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.17
DANN	Benign	0.58
PhyloP100		-1.1
PromoterAI		0.029	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3824830; hg19: chr10-120840661;