9-2270503-T-C

Position:

• chr9-2270503-T-C

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 0.54 in 151,892 control chromosomes in the GnomAD database, including 22,644 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 0.54 (22644 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 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: 0.540 AC: 81998 AN: 151774 Hom.: 22614 Cov.: 31

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.540 AC: 82086 AN: 151892 Hom.: 22644 Cov.: 31 AF XY: 0.546 AC XY: 40500 AN XY: 74206

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.877

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.544

Alfa AF: 0.499 Hom.: 9663

Bravo AF: 0.544

Asia WGS AF: 0.738 AC: 2565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.19
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7024139; hg19: chr9-2270503; COSMIC: COSV69442808;