chr7-95335328-A-T

Variant names:

• chr7-95335328-A-T
• rs2375001

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 0.256 in 152,184 control chromosomes in the GnomAD database, including 5,430 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 0.26 (5430 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.349 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: 0.256 AC: 38934 AN: 152066 Hom.: 5422 Cov.: 33

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.256 AC: 38958 AN: 152184 Hom.: 5430 Cov.: 33 AF XY: 0.264 AC XY: 19669 AN XY: 74402

African (AFR) AF: 0.227 AC: 9437 AN: 41500

American (AMR) AF: 0.212 AC: 3240 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3472

East Asian (EAS) AF: 0.139 AC: 723 AN: 5192

South Asian (SAS) AF: 0.363 AC: 1750 AN: 4818

European-Finnish (FIN) AF: 0.437 AC: 4621 AN: 10582

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17540 AN: 68004

Other (OTH) AF: 0.235 AC: 497 AN: 2112

Alfa AF: 0.157 Hom.: 333

Bravo AF: 0.233

Asia WGS AF: 0.261 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.83
PhyloP100		0.48
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: rs2375001; hg19: chr7-94964640;