rs916455

chr11-636929-C-T

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 0.0341 in 152,048 control chromosomes in the GnomAD database, including 169 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 0.034 (169 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0342 AC: 5200 AN: 151932 Hom.: 170 Cov.: 32

Gnomad AFR AF: 0.00844

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0345

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0587

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0366

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0341 AC: 5192 AN: 152048 Hom.: 169 Cov.: 32 AF XY: 0.0349 AC XY: 2591 AN XY: 74314

Gnomad4 AFR AF: 0.00841

Gnomad4 AMR AF: 0.0344

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.0581

Gnomad4 FIN AF: 0.0466

Gnomad4 NFE AF: 0.0366

Gnomad4 OTH AF: 0.0488

Alfa AF: 0.0301 Hom.: 17

Bravo AF: 0.0328

Asia WGS AF: 0.110 AC: 380 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.2
Dann	Benign	0.97

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs916455; hg19: chr11-636929;