rs11639988

Variant names:

• chr16-19933041-A-G
• rs11639988

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 0.155 in 151,984 control chromosomes in the GnomAD database, including 2,136 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 0.16 (2136 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 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: 0.155 AC: 23565 AN: 151866 Hom.: 2142 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0432

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.155 AC: 23584 AN: 151984 Hom.: 2136 Cov.: 31 AF XY: 0.150 AC XY: 11134 AN XY: 74288

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0440

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.139

Alfa AF: 0.141 Hom.: 831

Bravo AF: 0.160

Asia WGS AF: 0.0450 AC: 160 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11639988; hg19: chr16-19944363;