rs798646

Variant names:

• chr7-23580115-C-T
• rs798646

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 0.453 in 151,940 control chromosomes in the GnomAD database, including 15,777 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 0.45 (15777 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.902

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 (EAS) allele frequency at 95% confidence interval = 0.527 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: 0.454 AC: 68859 AN: 151822 Hom.: 15775 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.453 AC: 68871 AN: 151940 Hom.: 15777 Cov.: 31 AF XY: 0.460 AC XY: 34127 AN XY: 74248

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.438

Alfa AF: 0.427 Hom.: 28605

Bravo AF: 0.446

Asia WGS AF: 0.528 AC: 1830 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	0.49
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs798646; hg19: chr7-23619734;