rs916455

Variant names:

• chr11-636929-C-T
• rs916455

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 0.0341 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
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.00841 AC: 349 AN: 41482

American (AMR) AF: 0.0344 AC: 526 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0193 AC: 67 AN: 3470

East Asian (EAS) AF: 0.168 AC: 862 AN: 5128

South Asian (SAS) AF: 0.0581 AC: 280 AN: 4818

European-Finnish (FIN) AF: 0.0466 AC: 494 AN: 10604

Middle Eastern (MID) AF: 0.0479 AC: 14 AN: 292

European-Non Finnish (NFE) AF: 0.0366 AC: 2484 AN: 67952

Other (OTH) AF: 0.0488 AC: 103 AN: 2112

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
PhyloP100		-1.1
PromoterAI		0.032	Neutral

Splicing

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

Other links and lift over

dbSNP: rs916455; hg19: chr11-636929;