7-95326508-C-T

Variant names:

• chr7-95326508-C-T
• rs13236941

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 0.253 in 152,146 control chromosomes in the GnomAD database, including 6,220 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 0.25 (6220 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.448 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: 0.253 AC: 38471 AN: 152026 Hom.: 6216 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.138

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.253 AC: 38509 AN: 152146 Hom.: 6220 Cov.: 32 AF XY: 0.248 AC XY: 18465 AN XY: 74404

African (AFR) AF: 0.454 AC: 18810 AN: 41474

American (AMR) AF: 0.239 AC: 3648 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 541 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1839 AN: 5172

South Asian (SAS) AF: 0.171 AC: 823 AN: 4822

European-Finnish (FIN) AF: 0.123 AC: 1306 AN: 10604

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.162 AC: 10984 AN: 67994

Other (OTH) AF: 0.211 AC: 446 AN: 2112

Alfa AF: 0.195 Hom.: 2770

Bravo AF: 0.273

Asia WGS AF: 0.264 AC: 917 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	1.6
DANN	Benign	0.61
PhyloP100		0.082
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs13236941; hg19: chr7-94955820;