rs7937106

Variant names:

• chr11-107483586-T-C
• rs7937106

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 0.0506 in 152,232 control chromosomes in the GnomAD database, including 250 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 0.051 (250 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0831 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: 0.0506 AC: 7698 AN: 152114 Hom.: 249 Cov.: 32

Gnomad AFR AF: 0.0855

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0399

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.0763

Gnomad SAS AF: 0.0745

Gnomad FIN AF: 0.0484

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0308

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0506 AC: 7702 AN: 152232 Hom.: 250 Cov.: 32 AF XY: 0.0515 AC XY: 3833 AN XY: 74436

African (AFR) AF: 0.0854 AC: 3548 AN: 41528

American (AMR) AF: 0.0399 AC: 610 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0133 AC: 46 AN: 3470

East Asian (EAS) AF: 0.0759 AC: 393 AN: 5176

South Asian (SAS) AF: 0.0746 AC: 360 AN: 4826

European-Finnish (FIN) AF: 0.0484 AC: 513 AN: 10608

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0308 AC: 2094 AN: 68012

Other (OTH) AF: 0.0473 AC: 100 AN: 2112

Alfa AF: 0.0351 Hom.: 222

Bravo AF: 0.0503

Asia WGS AF: 0.0570 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.81
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs7937106; hg19: chr11-107354312;