rs4665788

Variant names:

• chr2-20965616-T-C
• rs4665788

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 0.784 in 152,216 control chromosomes in the GnomAD database, including 47,060 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 0.78 (47060 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.577
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 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: 0.784 AC: 119190 AN: 152098 Hom.: 47018 Cov.: 33

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.784 AC: 119285 AN: 152216 Hom.: 47060 Cov.: 33 AF XY: 0.784 AC XY: 58369 AN XY: 74410

African (AFR) AF: 0.853 AC: 35429 AN: 41540

American (AMR) AF: 0.737 AC: 11277 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2813 AN: 3468

East Asian (EAS) AF: 0.947 AC: 4904 AN: 5180

South Asian (SAS) AF: 0.840 AC: 4048 AN: 4818

European-Finnish (FIN) AF: 0.745 AC: 7890 AN: 10590

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50316 AN: 68002

Other (OTH) AF: 0.822 AC: 1734 AN: 2110

Alfa AF: 0.758 Hom.: 10596

Bravo AF: 0.788

Asia WGS AF: 0.877 AC: 3049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.92
DANN	Benign	0.58
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs4665788; hg19: chr2-21188488;