4-68672197-T-C

Variant names:

• chr4-68672197-T-C
• rs7686914

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 0.531 in 151,958 control chromosomes in the GnomAD database, including 21,842 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 0.53 (21842 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 10 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.602 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: 0.531 AC: 80586 AN: 151840 Hom.: 21799 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.531 AC: 80686 AN: 151958 Hom.: 21842 Cov.: 31 AF XY: 0.534 AC XY: 39687 AN XY: 74296

African (AFR) AF: 0.608 AC: 25193 AN: 41418

American (AMR) AF: 0.583 AC: 8906 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1576 AN: 3468

East Asian (EAS) AF: 0.561 AC: 2885 AN: 5140

South Asian (SAS) AF: 0.449 AC: 2162 AN: 4814

European-Finnish (FIN) AF: 0.553 AC: 5853 AN: 10578

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32409 AN: 67942

Other (OTH) AF: 0.534 AC: 1125 AN: 2108

Alfa AF: 0.369 Hom.: 974

Bravo AF: 0.537

Asia WGS AF: 0.481 AC: 1674 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	2.4
DANN	Benign	0.23
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7686914; hg19: chr4-69537915;