rs1724262

Variant names:

• chr7-106851232-A-G
• rs1724262

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 0.655 in 152,084 control chromosomes in the GnomAD database, including 33,100 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 0.65 (33100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 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: 0.655 AC: 99510 AN: 151966 Hom.: 33060 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.655 AC: 99611 AN: 152084 Hom.: 33100 Cov.: 32 AF XY: 0.657 AC XY: 48864 AN XY: 74326

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.963

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.657

Alfa AF: 0.626 Hom.: 15003

Bravo AF: 0.652

Asia WGS AF: 0.801 AC: 2785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.078
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1724262; hg19: chr7-106491677;