rs2096735

Positions:

• chr11-96992442-G-A
• chr11-96992442-G-C

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 0.441 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.435

Alfa AF: 0.331 Hom.: 10982

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2096735; hg19: chr11-96863442;