rs9542456

Variant names:

• chr13-70644514-T-C
• rs9542456

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 0.696 in 151,966 control chromosomes in the GnomAD database, including 37,590 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 0.70 (37590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 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: 0.696 AC: 105626 AN: 151848 Hom.: 37545 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.696 AC: 105732 AN: 151966 Hom.: 37590 Cov.: 32 AF XY: 0.690 AC XY: 51214 AN XY: 74254

African (AFR) AF: 0.856 AC: 35500 AN: 41466

American (AMR) AF: 0.686 AC: 10457 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2310 AN: 3466

East Asian (EAS) AF: 0.632 AC: 3266 AN: 5170

South Asian (SAS) AF: 0.617 AC: 2980 AN: 4830

European-Finnish (FIN) AF: 0.537 AC: 5661 AN: 10540

Middle Eastern (MID) AF: 0.705 AC: 206 AN: 292

European-Non Finnish (NFE) AF: 0.637 AC: 43262 AN: 67938

Other (OTH) AF: 0.681 AC: 1436 AN: 2110

Alfa AF: 0.676 Hom.: 55728

Bravo AF: 0.714

Asia WGS AF: 0.610 AC: 2123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.50
DANN	Benign	0.74
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9542456; hg19: chr13-71218646;