chr9-7540496-G-T

Variant names:

• chr9-7540496-G-T
• rs12349302

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.113 in 152,204 control chromosomes in the GnomAD database, including 1,338 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 0.11 (1338 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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: 0.113 AC: 17162 AN: 152086 Hom.: 1333 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0692

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0267

Gnomad FIN AF: 0.0877

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.0845

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.113 AC: 17195 AN: 152204 Hom.: 1338 Cov.: 33 AF XY: 0.109 AC XY: 8112 AN XY: 74416

African (AFR) AF: 0.213 AC: 8846 AN: 41510

American (AMR) AF: 0.0692 AC: 1058 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0536 AC: 186 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0267 AC: 129 AN: 4830

European-Finnish (FIN) AF: 0.0877 AC: 930 AN: 10600

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.0845 AC: 5743 AN: 68000

Other (OTH) AF: 0.0848 AC: 179 AN: 2112

Alfa AF: 0.0897 Hom.: 889

Bravo AF: 0.117

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	13
DANN	Benign	0.46
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs12349302; hg19: chr9-7540496;