7-125965048-T-C

Variant names:

• chr7-125965048-T-C
• rs4357236

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 0.313 in 151,796 control chromosomes in the GnomAD database, including 8,244 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 0.31 (8244 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.476 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: 0.313 AC: 47438 AN: 151676 Hom.: 8232 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.313 AC: 47465 AN: 151796 Hom.: 8244 Cov.: 32 AF XY: 0.314 AC XY: 23285 AN XY: 74174

Gnomad4 AFR AF: 0.174 AC: 0.1744 AN: 0.1744

Gnomad4 AMR AF: 0.485 AC: 0.48491 AN: 0.48491

Gnomad4 ASJ AF: 0.443 AC: 0.443195 AN: 0.443195

Gnomad4 EAS AF: 0.355 AC: 0.355207 AN: 0.355207

Gnomad4 SAS AF: 0.412 AC: 0.412168 AN: 0.412168

Gnomad4 FIN AF: 0.288 AC: 0.288421 AN: 0.288421

Gnomad4 NFE AF: 0.345 AC: 0.344883 AN: 0.344883

Gnomad4 OTH AF: 0.360 AC: 0.36019 AN: 0.36019

Alfa AF: 0.309 Hom.: 1028

Bravo AF: 0.323

Asia WGS AF: 0.357 AC: 1239 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4357236; hg19: chr7-125605102;