rs9940021

chr16-26285275-G-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 0.461 in 151,882 control chromosomes in the GnomAD database, including 16,344 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 0.46 (16344 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

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 (AFR) allele frequency at 95% confidence interval = 0.512 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: 0.461 AC: 69971 AN: 151764 Hom.: 16319 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.461 AC: 70043 AN: 151882 Hom.: 16344 Cov.: 32 AF XY: 0.456 AC XY: 33834 AN XY: 74216

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.451

Alfa AF: 0.461 Hom.: 1977

Bravo AF: 0.467

Asia WGS AF: 0.359 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.8
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9940021; hg19: chr16-26296596;