4-118019712-C-A

Variant names:

• chr4-118019712-C-A
• rs1994385

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 0.675 in 151,304 control chromosomes in the GnomAD database, including 36,388 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 0.68 (36388 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.795 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: 0.675 AC: 102067 AN: 151186 Hom.: 36359 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.675 AC: 102137 AN: 151304 Hom.: 36388 Cov.: 31 AF XY: 0.682 AC XY: 50423 AN XY: 73974

African (AFR) AF: 0.433 AC: 17925 AN: 41388

American (AMR) AF: 0.770 AC: 11677 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2593 AN: 3454

East Asian (EAS) AF: 0.746 AC: 3852 AN: 5166

South Asian (SAS) AF: 0.816 AC: 3934 AN: 4820

European-Finnish (FIN) AF: 0.784 AC: 8278 AN: 10564

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.765 AC: 51605 AN: 67452

Other (OTH) AF: 0.663 AC: 1392 AN: 2098

Alfa AF: 0.731 Hom.: 6863

Bravo AF: 0.660

Asia WGS AF: 0.770 AC: 2660 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.061
DANN	Benign	0.39
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs1994385; hg19: chr4-118940867;