7-9612650-C-T

Variant names:

• chr7-9612650-C-T
• rs1032873

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 0.414 in 152,032 control chromosomes in the GnomAD database, including 14,852 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 0.41 (14852 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 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: 0.414 AC: 62901 AN: 151914 Hom.: 14850 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.414 AC: 62908 AN: 152032 Hom.: 14852 Cov.: 32 AF XY: 0.419 AC XY: 31101 AN XY: 74304

African (AFR) AF: 0.182 AC: 7567 AN: 41492

American (AMR) AF: 0.409 AC: 6249 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1721 AN: 3470

East Asian (EAS) AF: 0.712 AC: 3675 AN: 5158

South Asian (SAS) AF: 0.472 AC: 2278 AN: 4822

European-Finnish (FIN) AF: 0.572 AC: 6028 AN: 10540

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 34009 AN: 67970

Other (OTH) AF: 0.439 AC: 927 AN: 2110

Alfa AF: 0.469 Hom.: 68519

Bravo AF: 0.392

Asia WGS AF: 0.600 AC: 2080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.56
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs1032873; hg19: chr7-9652280;