rs6724422

Variant names:

• chr2-67749656-C-T
• rs6724422

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 0.0643 in 151,984 control chromosomes in the GnomAD database, including 392 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 0.064 (392 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0948 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: 0.0642 AC: 9753 AN: 151868 Hom.: 391 Cov.: 32

Gnomad AFR AF: 0.0972

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.0457

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0179

Gnomad FIN AF: 0.0449

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0620

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0643 AC: 9765 AN: 151984 Hom.: 392 Cov.: 32 AF XY: 0.0617 AC XY: 4587 AN XY: 74296

African (AFR) AF: 0.0973 AC: 4028 AN: 41398

American (AMR) AF: 0.0457 AC: 697 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0331 AC: 115 AN: 3472

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5174

South Asian (SAS) AF: 0.0177 AC: 85 AN: 4806

European-Finnish (FIN) AF: 0.0449 AC: 475 AN: 10572

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0620 AC: 4214 AN: 67982

Other (OTH) AF: 0.0578 AC: 122 AN: 2110

Alfa AF: 0.0614 Hom.: 402

Bravo AF: 0.0647

Asia WGS AF: 0.0170 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs6724422; hg19: chr2-67976788;