rs2639889

chr16-61089243-C-T

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 0.615 in 151,820 control chromosomes in the GnomAD database, including 28,772 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 0.62 (28772 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 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: 0.615 AC: 93312 AN: 151700 Hom.: 28730 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.615 AC: 93413 AN: 151820 Hom.: 28772 Cov.: 31 AF XY: 0.611 AC XY: 45346 AN XY: 74190

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.591

Alfa AF: 0.613 Hom.: 42660

Bravo AF: 0.614

Asia WGS AF: 0.642 AC: 2233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	16
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2639889; hg19: chr16-61123147;