rs4810837

Variant names:

• chr20-48612619-T-G
• rs4810837
• ENST00000775767.1:n.131+9055A>C

Variant summary

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

The ENST00000775767.1(ENSG00000301042):​n.131+9055A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,062 control chromosomes in the GnomAD database, including 12,147 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 0.40 (12147 hom., cov: 33)
• Consequence: ENSG00000301042 ENST00000775767.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 5 publications found

Genes affected

ENSG00000301042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.5 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
ENSG00000301042	ENST00000775767.1	n.131+9055A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60369 AN: 151944 Hom.: 12127 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.397 AC: 60433 AN: 152062 Hom.: 12147 Cov.: 33 AF XY: 0.395 AC XY: 29346 AN XY: 74338

African (AFR) AF: 0.397 AC: 16455 AN: 41468

American (AMR) AF: 0.444 AC: 6791 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1478 AN: 3472

East Asian (EAS) AF: 0.345 AC: 1782 AN: 5172

South Asian (SAS) AF: 0.517 AC: 2487 AN: 4808

European-Finnish (FIN) AF: 0.327 AC: 3462 AN: 10576

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26551 AN: 67966

Other (OTH) AF: 0.425 AC: 896 AN: 2108

Alfa AF: 0.397 Hom.: 32288

Bravo AF: 0.402

Asia WGS AF: 0.419 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs4810837; hg19: chr20-47229157;