rs4686162

Variant names:

• chr3-7816463-T-C
• rs4686162

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 0.143 in 152,094 control chromosomes in the GnomAD database, including 1,851 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 0.14 (1851 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.198 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: 0.143 AC: 21687 AN: 151976 Hom.: 1849 Cov.: 32

Gnomad AFR AF: 0.0616

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.00405

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.143 AC: 21687 AN: 152094 Hom.: 1851 Cov.: 32 AF XY: 0.140 AC XY: 10381 AN XY: 74368

African (AFR) AF: 0.0614 AC: 2550 AN: 41524

American (AMR) AF: 0.116 AC: 1778 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3466

East Asian (EAS) AF: 0.00406 AC: 21 AN: 5172

South Asian (SAS) AF: 0.187 AC: 901 AN: 4824

European-Finnish (FIN) AF: 0.157 AC: 1664 AN: 10586

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.201 AC: 13628 AN: 67946

Other (OTH) AF: 0.143 AC: 301 AN: 2110

Alfa AF: 0.180 Hom.: 4367

Bravo AF: 0.131

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.61
DANN	Benign	0.68
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs4686162; hg19: chr3-7858150;