chr9-21199681-G-T

Position:

• chr9-21199681-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 0.312 in 151,766 control chromosomes in the GnomAD database, including 9,390 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 0.31 (9390 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 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: 0.313 AC: 47393 AN: 151650 Hom.: 9392 Cov.: 31

Gnomad AFR AF: 0.0782

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.312 AC: 47378 AN: 151766 Hom.: 9390 Cov.: 31 AF XY: 0.312 AC XY: 23143 AN XY: 74140

Gnomad4 AFR AF: 0.0779

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.324

Alfa AF: 0.411 Hom.: 17712

Bravo AF: 0.293

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4977686; hg19: chr9-21199680; COSMIC: COSV53330746;