chr7-50273756-G-A

Variant names:

• chr7-50273756-G-A
• rs10276619

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 0.59 in 152,048 control chromosomes in the GnomAD database, including 27,040 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 0.59 (27040 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.708 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: 0.590 AC: 89590 AN: 151930 Hom.: 27007 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.590 AC: 89673 AN: 152048 Hom.: 27040 Cov.: 32 AF XY: 0.594 AC XY: 44115 AN XY: 74298

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.609

Alfa AF: 0.626 Hom.: 43660

Bravo AF: 0.583

Asia WGS AF: 0.640 AC: 2224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.12
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10276619; hg19: chr7-50313352;