rs7125774

Variant names:

• chr11-13597257-C-T
• rs7125774

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 0.614 in 152,056 control chromosomes in the GnomAD database, including 28,801 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 0.61 (28801 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.708 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: 0.614 AC: 93274 AN: 151940 Hom.: 28763 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.614 AC: 93367 AN: 152056 Hom.: 28801 Cov.: 32 AF XY: 0.616 AC XY: 45813 AN XY: 74318

African (AFR) AF: 0.582 AC: 24136 AN: 41462

American (AMR) AF: 0.606 AC: 9264 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2444 AN: 3464

East Asian (EAS) AF: 0.535 AC: 2759 AN: 5158

South Asian (SAS) AF: 0.728 AC: 3508 AN: 4816

European-Finnish (FIN) AF: 0.634 AC: 6699 AN: 10574

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.626 AC: 42542 AN: 67974

Other (OTH) AF: 0.611 AC: 1292 AN: 2114

Alfa AF: 0.620 Hom.: 42441

Bravo AF: 0.603

Asia WGS AF: 0.637 AC: 2216 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	0.52
DANN	Benign	0.66
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7125774; hg19: chr11-13618804;