rs763873

Variant names:

• chr7-48953756-T-C
• rs763873

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 0.116 in 152,174 control chromosomes in the GnomAD database, including 1,522 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 0.12 (1522 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 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: 0.116 AC: 17615 AN: 152058 Hom.: 1516 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0753

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.0667

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0629

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.116 AC: 17651 AN: 152174 Hom.: 1522 Cov.: 33 AF XY: 0.114 AC XY: 8444 AN XY: 74386

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.0751

Gnomad4 ASJ AF: 0.0424

Gnomad4 EAS AF: 0.0667

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.0436

Gnomad4 NFE AF: 0.0629

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0952 Hom.: 279

Bravo AF: 0.123

Asia WGS AF: 0.131 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs763873; hg19: chr7-48993352;