rs4690290

Variant names:

• chr4-695713-G-C
• rs4690290

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 0.54 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.616 AC: 25446 AN: 41340

American (AMR) AF: 0.563 AC: 8573 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2049 AN: 3466

East Asian (EAS) AF: 0.325 AC: 1634 AN: 5022

South Asian (SAS) AF: 0.385 AC: 1848 AN: 4806

European-Finnish (FIN) AF: 0.592 AC: 6232 AN: 10532

Middle Eastern (MID) AF: 0.503 AC: 146 AN: 290

European-Non Finnish (NFE) AF: 0.506 AC: 34341 AN: 67878

Other (OTH) AF: 0.545 AC: 1147 AN: 2106

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs4690290; hg19: chr4-689502;