rs4668497

Variant names:

• chr2-6459839-T-C
• rs4668497

Your query was ambiguous. Multiple possible variants found:

• chr2-6459839-T-C
• chr2-6459839-T-G

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 0.461 in 151,536 control chromosomes in the GnomAD database, including 16,637 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 0.46 (16637 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.533 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: 0.461 AC: 69775 AN: 151420 Hom.: 16640 Cov.: 29

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.461 AC: 69809 AN: 151536 Hom.: 16637 Cov.: 29 AF XY: 0.471 AC XY: 34850 AN XY: 74008

African (AFR) AF: 0.368 AC: 15198 AN: 41288

American (AMR) AF: 0.543 AC: 8280 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1386 AN: 3466

East Asian (EAS) AF: 0.536 AC: 2731 AN: 5098

South Asian (SAS) AF: 0.547 AC: 2609 AN: 4774

European-Finnish (FIN) AF: 0.671 AC: 7008 AN: 10450

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.458 AC: 31076 AN: 67902

Other (OTH) AF: 0.429 AC: 905 AN: 2108

Alfa AF: 0.341 Hom.: 1118

Bravo AF: 0.448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.49
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4668497; hg19: chr2-6599971;