rs7926262

Variant names:

• chr11-23607016-T-C
• rs7926262

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 0.0464 in 152,316 control chromosomes in the GnomAD database, including 205 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 0.046 (205 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0594 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: 0.0463 AC: 7053 AN: 152198 Hom.: 206 Cov.: 33

Gnomad AFR AF: 0.0614

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0281

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.0167

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0520

Gnomad OTH AF: 0.0483

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

GnomAD4 genome AF: 0.0464 AC: 7061 AN: 152316 Hom.: 205 Cov.: 33 AF XY: 0.0444 AC XY: 3304 AN XY: 74474

Gnomad4 AFR AF: 0.0614

Gnomad4 AMR AF: 0.0280

Gnomad4 ASJ AF: 0.0334

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0178

Gnomad4 FIN AF: 0.0167

Gnomad4 NFE AF: 0.0521

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0485 Hom.: 120

Bravo AF: 0.0478

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7926262; hg19: chr11-23628562;