9-21199681-G-T

Variant names:

• chr9-21199681-G-T
• rs4977686

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 0.312 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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0779 AC: 3220 AN: 41334

American (AMR) AF: 0.332 AC: 5067 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1481 AN: 3464

East Asian (EAS) AF: 0.145 AC: 750 AN: 5158

South Asian (SAS) AF: 0.289 AC: 1394 AN: 4820

European-Finnish (FIN) AF: 0.440 AC: 4623 AN: 10516

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29661 AN: 67914

Other (OTH) AF: 0.324 AC: 681 AN: 2100

Alfa AF: 0.408 Hom.: 20820

Bravo AF: 0.293

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.51
PhyloP100		-0.45

Splicing

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

Other links and lift over

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