4-3764538-T-C

Variant names:

• chr4-3764538-T-C
• rs6846820

Variant summary

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

The variant allele was found at a frequency of 0.896 in 152,292 control chromosomes in the GnomAD database, including 61,617 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 0.90 (61617 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.36
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.97 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

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136330 AN: 152174 Hom.: 61553 Cov.: 35

Gnomad AFR AF: 0.978

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.896 AC: 136454 AN: 152292 Hom.: 61617 Cov.: 35 AF XY: 0.891 AC XY: 66312 AN XY: 74450

African (AFR) AF: 0.978 AC: 40660 AN: 41576

American (AMR) AF: 0.806 AC: 12336 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3079 AN: 3472

East Asian (EAS) AF: 0.623 AC: 3212 AN: 5154

South Asian (SAS) AF: 0.779 AC: 3755 AN: 4820

European-Finnish (FIN) AF: 0.883 AC: 9374 AN: 10618

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.897 AC: 61015 AN: 68026

Other (OTH) AF: 0.900 AC: 1905 AN: 2116

Alfa AF: 0.903 Hom.: 8033

Bravo AF: 0.894

Asia WGS AF: 0.723 AC: 2515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.070
DANN	Benign	0.29
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs6846820; hg19: chr4-3766265;