16-61089243-C-T

Variant names:

• chr16-61089243-C-T
• rs2639889

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 0.615 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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.653 AC: 27035 AN: 41432

American (AMR) AF: 0.559 AC: 8521 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2315 AN: 3470

East Asian (EAS) AF: 0.681 AC: 3497 AN: 5138

South Asian (SAS) AF: 0.515 AC: 2479 AN: 4812

European-Finnish (FIN) AF: 0.592 AC: 6201 AN: 10482

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.608 AC: 41297 AN: 67920

Other (OTH) AF: 0.591 AC: 1245 AN: 2108

Alfa AF: 0.612 Hom.: 58505

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2639889; hg19: chr16-61123147;