rs6724422

Positions:

• chr2-67749656-C-T

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 0.0643 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0973

Gnomad4 AMR AF: 0.0457

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0177

Gnomad4 FIN AF: 0.0449

Gnomad4 NFE AF: 0.0620

Gnomad4 OTH AF: 0.0578

Alfa AF: 0.0580 Hom.: 241

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6724422; hg19: chr2-67976788;