rs11647994

chr16-36034953-A-G

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 0.328 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.0903

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.356

Alfa AF: 0.391 Hom.: 3324

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

Publications

LitVar

Other links and lift over

dbSNP: rs11647994; hg19: chr16-35269324;