4-695713-G-C

Position:

• chr4-695713-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.54 in 151,588 control chromosomes in the GnomAD database, including 22,585 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 (22585 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81729 AN: 151468 Hom.: 22529 Cov.: 30

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.540 AC: 81848 AN: 151588 Hom.: 22585 Cov.: 30 AF XY: 0.543 AC XY: 40223 AN XY: 74056

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.545

Alfa AF: 0.530 Hom.: 2645

Bravo AF: 0.546

Asia WGS AF: 0.380 AC: 1326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.78
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4690290; hg19: chr4-689502;