7-97095273-C-T

Variant names:

• chr7-97095273-C-T
• rs1343645

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 0.146 in 152,100 control chromosomes in the GnomAD database, including 1,874 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 0.15 (1874 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 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: 0.146 AC: 22179 AN: 151982 Hom.: 1872 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0769

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.146 AC: 22204 AN: 152100 Hom.: 1874 Cov.: 32 AF XY: 0.152 AC XY: 11271 AN XY: 74338

African (AFR) AF: 0.136 AC: 5635 AN: 41494

American (AMR) AF: 0.232 AC: 3541 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3472

East Asian (EAS) AF: 0.359 AC: 1849 AN: 5154

South Asian (SAS) AF: 0.214 AC: 1031 AN: 4818

European-Finnish (FIN) AF: 0.129 AC: 1370 AN: 10584

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7835 AN: 67982

Other (OTH) AF: 0.156 AC: 330 AN: 2116

Alfa AF: 0.126 Hom.: 5279

Bravo AF: 0.156

Asia WGS AF: 0.300 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.66
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1343645; hg19: chr7-96724585;