7-50264865-C-T

Position:

• chr7-50264865-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 0.667 in 151,966 control chromosomes in the GnomAD database, including 34,332 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 0.67 (34332 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.794 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: 0.667 AC: 101324 AN: 151850 Hom.: 34298 Cov.: 30

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.667 AC: 101412 AN: 151966 Hom.: 34332 Cov.: 30 AF XY: 0.672 AC XY: 49893 AN XY: 74286

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.665

Alfa AF: 0.680 Hom.: 60757

Bravo AF: 0.657

Asia WGS AF: 0.687 AC: 2388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1456896; hg19: chr7-50304461;