7-50264865-C-T

Variant names:

• chr7-50264865-C-T
• rs1456896

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;