rs11644988

Variant names:

• chr16-86451525-G-A
• rs11644988

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 0.081 in 152,214 control chromosomes in the GnomAD database, including 787 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 0.081 (787 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.246 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: 0.0810 AC: 12317 AN: 152096 Hom.: 785 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0368

Gnomad ASJ AF: 0.0478

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.0299

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0489

Gnomad OTH AF: 0.0808

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

GnomAD4 genome AF: 0.0810 AC: 12332 AN: 152214 Hom.: 787 Cov.: 32 AF XY: 0.0784 AC XY: 5837 AN XY: 74434

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0368

Gnomad4 ASJ AF: 0.0478

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.0245

Gnomad4 FIN AF: 0.0299

Gnomad4 NFE AF: 0.0488

Gnomad4 OTH AF: 0.0804

Alfa AF: 0.0785 Hom.: 113

Bravo AF: 0.0875

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11644988; hg19: chr16-86485131;