7-50266267-T-G

Position:

• chr7-50266267-T-G

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 0.269 in 152,252 control chromosomes in the GnomAD database, including 6,833 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 0.27 (6833 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.906

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.47 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: 0.269 AC: 40881 AN: 152134 Hom.: 6829 Cov.: 33

Gnomad AFR AF: 0.0850

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.269 AC: 40895 AN: 152252 Hom.: 6833 Cov.: 33 AF XY: 0.273 AC XY: 20344 AN XY: 74444

Gnomad4 AFR AF: 0.0849

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.294

Alfa AF: 0.320 Hom.: 18837

Bravo AF: 0.274

Asia WGS AF: 0.258 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4917014; hg19: chr7-50305863;