rs346062

Variant names:

• chr19-43694425-G-A
• rs346062
• ENST00000636801.1:n.299-625G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000636801.1(ENSG00000283525):​n.299-625G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,006 control chromosomes in the GnomAD database, including 29,045 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 0.61 (29045 hom., cov: 31)
• Consequence: ENSG00000283525 ENST00000636801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.82
• Publications: 3 publications found

Genes affected

ENSG00000283525 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372412	NR_172891.1	n.965-625G>A		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283525	ENST00000636801.1	n.299-625G>A		intron_variant	Intron 2 of 5	6
ENSG00000290609	ENST00000637093.1	n.139-625G>A		intron_variant	Intron 1 of 4	5
ENSG00000290609	ENST00000737707.1	n.35-625G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93051 AN: 151888 Hom.: 29015 Cov.: 31

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.613 AC: 93134 AN: 152006 Hom.: 29045 Cov.: 31 AF XY: 0.612 AC XY: 45474 AN XY: 74312

African (AFR) AF: 0.735 AC: 30485 AN: 41458

American (AMR) AF: 0.556 AC: 8473 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1795 AN: 3472

East Asian (EAS) AF: 0.574 AC: 2969 AN: 5172

South Asian (SAS) AF: 0.536 AC: 2591 AN: 4830

European-Finnish (FIN) AF: 0.589 AC: 6216 AN: 10556

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38636 AN: 67962

Other (OTH) AF: 0.594 AC: 1251 AN: 2106

Alfa AF: 0.599 Hom.: 4699

Bravo AF: 0.613

Asia WGS AF: 0.551 AC: 1918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0050
DANN	Benign	0.45
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs346062; hg19: chr19-44198577;