rs11647994

Variant names:

• chr16-36034953-A-G
• rs11647994

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 0.328 in 149,970 control chromosomes in the GnomAD database, including 10,153 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 0.33 (10153 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 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: 0.328 AC: 49203 AN: 149852 Hom.: 10150 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.0901

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.328 AC: 49213 AN: 149970 Hom.: 10153 Cov.: 32 AF XY: 0.322 AC XY: 23567 AN XY: 73198

African (AFR) AF: 0.103 AC: 4225 AN: 41108

American (AMR) AF: 0.436 AC: 6493 AN: 14876

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1611 AN: 3430

East Asian (EAS) AF: 0.0903 AC: 456 AN: 5048

South Asian (SAS) AF: 0.224 AC: 1078 AN: 4814

European-Finnish (FIN) AF: 0.360 AC: 3806 AN: 10576

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30278 AN: 66842

Other (OTH) AF: 0.356 AC: 739 AN: 2074

Alfa AF: 0.382 Hom.: 3566

Bravo AF: 0.328

Asia WGS AF: 0.145 AC: 509 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.35

Splicing

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

Other links and lift over

dbSNP: rs11647994; hg19: chr16-35269324;