4-68671436-A-C

Variant names:

• chr4-68671436-A-C
• rs1960773

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 0.537 in 146,526 control chromosomes in the GnomAD database, including 21,553 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 0.54 (21553 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 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: 0.537 AC: 78655 AN: 146414 Hom.: 21510 Cov.: 25

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.537 AC: 78756 AN: 146526 Hom.: 21553 Cov.: 25 AF XY: 0.540 AC XY: 38509 AN XY: 71354

African (AFR) AF: 0.610 AC: 24100 AN: 39512

American (AMR) AF: 0.582 AC: 8514 AN: 14636

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1542 AN: 3306

East Asian (EAS) AF: 0.552 AC: 2708 AN: 4904

South Asian (SAS) AF: 0.442 AC: 2039 AN: 4608

European-Finnish (FIN) AF: 0.568 AC: 5651 AN: 9946

Middle Eastern (MID) AF: 0.476 AC: 136 AN: 286

European-Non Finnish (NFE) AF: 0.490 AC: 32552 AN: 66408

Other (OTH) AF: 0.534 AC: 1078 AN: 2018

Alfa AF: 0.378 Hom.: 847

Bravo AF: 0.545

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.22
PhyloP100		-3.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1960773; hg19: chr4-69537154;