9-2270503-T-C

Variant names:

• chr9-2270503-T-C
• rs7024139

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;