rs9940021

Variant names:

• chr16-26285275-G-T
• rs9940021

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;