rs404801

Variant names:

• chr3-83402210-A-C
• rs404801
• ENST00000670186.1:n.143-10333A>C

Variant summary

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

The ENST00000670186.1(ENSG00000288004):​n.143-10333A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,968 control chromosomes in the GnomAD database, including 15,307 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 0.44 (15307 hom., cov: 32)
• Consequence: ENSG00000288004 ENST00000670186.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68
• Publications: 2 publications found

Genes affected

ENSG00000288004 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377181	XR_941003.3	n.231+1245T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288004	ENST00000670186.1	n.143-10333A>C		intron_variant	Intron 1 of 2
ENSG00000288004	ENST00000780115.1	n.96-1257A>C		intron_variant	Intron 1 of 2
ENSG00000301615	ENST00000780184.1	n.183+1245T>G		intron_variant	Intron 2 of 2
ENSG00000301615	ENST00000780185.1	n.361+1245T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67501 AN: 151850 Hom.: 15274 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.436

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.445 AC: 67590 AN: 151968 Hom.: 15307 Cov.: 32 AF XY: 0.442 AC XY: 32818 AN XY: 74262

African (AFR) AF: 0.521 AC: 21593 AN: 41448

American (AMR) AF: 0.386 AC: 5891 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1462 AN: 3464

East Asian (EAS) AF: 0.210 AC: 1087 AN: 5170

South Asian (SAS) AF: 0.461 AC: 2223 AN: 4824

European-Finnish (FIN) AF: 0.427 AC: 4501 AN: 10534

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29360 AN: 67946

Other (OTH) AF: 0.440 AC: 927 AN: 2108

Alfa AF: 0.441 Hom.: 2865

Bravo AF: 0.442

Asia WGS AF: 0.341 AC: 1186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.17
DANN	Benign	0.81
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs404801; hg19: chr3-83451361;