chr7-23580115-C-T

Variant names:

• chr7-23580115-C-T
• rs798646

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.459 AC: 19008 AN: 41422

American (AMR) AF: 0.442 AC: 6730 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1066 AN: 3464

East Asian (EAS) AF: 0.544 AC: 2820 AN: 5184

South Asian (SAS) AF: 0.523 AC: 2520 AN: 4816

European-Finnish (FIN) AF: 0.548 AC: 5773 AN: 10534

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29325 AN: 67980

Other (OTH) AF: 0.438 AC: 923 AN: 2106

Alfa AF: 0.431 Hom.: 59985

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
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs798646; hg19: chr7-23619734;