chr7-95349745-C-T

Position:

• chr7-95349745-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0278 in 152,240 control chromosomes in the GnomAD database, including 112 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 0.028 (112 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0276 AC: 4206 AN: 152122 Hom.: 108 Cov.: 32

Gnomad AFR AF: 0.0671

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0173

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.0281

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0285

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00792

Gnomad OTH AF: 0.0215

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

GnomAD4 genome AF: 0.0278 AC: 4231 AN: 152240 Hom.: 112 Cov.: 32 AF XY: 0.0283 AC XY: 2104 AN XY: 74426

Gnomad4 AFR AF: 0.0675

Gnomad4 AMR AF: 0.0173

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.0284

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.0285

Gnomad4 NFE AF: 0.00792

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.0226 Hom.: 7

Bravo AF: 0.0287

Asia WGS AF: 0.0430 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487129; hg19: chr7-94979057;