chr9-21258475-G-T

Variant names:

• chr9-21258475-G-T
• rs10964938

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 0.2 in 152,076 control chromosomes in the GnomAD database, including 3,234 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 0.20 (3234 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 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: 0.200 AC: 30361 AN: 151960 Hom.: 3232 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.200 AC: 30385 AN: 152076 Hom.: 3234 Cov.: 32 AF XY: 0.201 AC XY: 14918 AN XY: 74334

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.196

Alfa AF: 0.202 Hom.: 560

Bravo AF: 0.206

Asia WGS AF: 0.241 AC: 837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10964938; hg19: chr9-21258474;