rs346578

Variant names:

• chr13-42608851-G-A
• rs346578

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 0.0594 in 152,206 control chromosomes in the GnomAD database, including 278 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 0.059 (278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0717 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: 0.0594 AC: 9041 AN: 152088 Hom.: 278 Cov.: 32

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0432

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0615

Gnomad FIN AF: 0.0879

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0734

Gnomad OTH AF: 0.0544

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

GnomAD4 genome AF: 0.0594 AC: 9048 AN: 152206 Hom.: 278 Cov.: 32 AF XY: 0.0584 AC XY: 4348 AN XY: 74420

African (AFR) AF: 0.0481 AC: 1996 AN: 41536

American (AMR) AF: 0.0430 AC: 658 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5176

South Asian (SAS) AF: 0.0615 AC: 297 AN: 4828

European-Finnish (FIN) AF: 0.0879 AC: 930 AN: 10586

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0734 AC: 4994 AN: 68000

Other (OTH) AF: 0.0539 AC: 114 AN: 2116

Alfa AF: 0.0645 Hom.: 583

Bravo AF: 0.0541

Asia WGS AF: 0.0280 AC: 100 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	0.16
DANN	Benign	0.50
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs346578; hg19: chr13-43182987;