11-96992442-G-A

Variant names:

• chr11-96992442-G-A
• rs2096735

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 0.441 in 151,936 control chromosomes in the GnomAD database, including 16,767 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 0.44 (16767 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 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: 0.441 AC: 66877 AN: 151818 Hom.: 16719 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.442

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.441 AC: 66991 AN: 151936 Hom.: 16767 Cov.: 32 AF XY: 0.441 AC XY: 32783 AN XY: 74272

African (AFR) AF: 0.691 AC: 28625 AN: 41428

American (AMR) AF: 0.370 AC: 5641 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3470

East Asian (EAS) AF: 0.502 AC: 2586 AN: 5156

South Asian (SAS) AF: 0.448 AC: 2157 AN: 4814

European-Finnish (FIN) AF: 0.349 AC: 3675 AN: 10542

Middle Eastern (MID) AF: 0.455 AC: 132 AN: 290

European-Non Finnish (NFE) AF: 0.318 AC: 21580 AN: 67950

Other (OTH) AF: 0.435 AC: 919 AN: 2112

Alfa AF: 0.347 Hom.: 15857

Bravo AF: 0.451

Asia WGS AF: 0.512 AC: 1781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.44
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs2096735; hg19: chr11-96863442;