11-95968431-T-G

Variant names:

• chr11-95968431-T-G
• rs1893057

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 0.301 in 152,108 control chromosomes in the GnomAD database, including 7,104 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 0.30 (7104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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 (SAS) allele frequency at 95% confidence interval = 0.424 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: 0.301 AC: 45746 AN: 151990 Hom.: 7102 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.301 AC: 45769 AN: 152108 Hom.: 7104 Cov.: 32 AF XY: 0.305 AC XY: 22684 AN XY: 74360

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.286

Alfa AF: 0.282 Hom.: 3098

Bravo AF: 0.301

Asia WGS AF: 0.402 AC: 1396 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	0.58
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1893057; hg19: chr11-95701595;