rs34974495

Variant names:

• chr18-60373556-G-A
• rs34974495
• ENST00000650201.1:n.113+44211G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000650201.1(ENSG00000285681):​n.113+44211G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 149,920 control chromosomes in the GnomAD database, including 13 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 0.015 (13 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 4 publications found

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0149 (2241/149920) while in subpopulation SAS AF = 0.0243 (116/4766). AF 95% confidence interval is 0.0207. There are 13 homozygotes in GnomAd4. There are 1056 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 13 gene

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
ENSG00000285681	ENST00000650201.1	n.113+44211G>A		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+44211G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0150 AC: 2240 AN: 149808 Hom.: 13 Cov.: 32

Gnomad AFR AF: 0.0158

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00532

Gnomad ASJ AF: 0.00289

Gnomad EAS AF: 0.00156

Gnomad SAS AF: 0.0251

Gnomad FIN AF: 0.0125

Gnomad MID AF: 0.00968

Gnomad NFE AF: 0.0182

Gnomad OTH AF: 0.0106

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

GnomAD4 genome AF: 0.0149 AC: 2241 AN: 149920 Hom.: 13 Cov.: 32 AF XY: 0.0145 AC XY: 1056 AN XY: 72980

African (AFR) AF: 0.0159 AC: 643 AN: 40528

American (AMR) AF: 0.00531 AC: 80 AN: 15056

Ashkenazi Jewish (ASJ) AF: 0.00289 AC: 10 AN: 3466

East Asian (EAS) AF: 0.00156 AC: 8 AN: 5124

South Asian (SAS) AF: 0.0243 AC: 116 AN: 4766

European-Finnish (FIN) AF: 0.0125 AC: 124 AN: 9930

Middle Eastern (MID) AF: 0.0105 AC: 3 AN: 286

European-Non Finnish (NFE) AF: 0.0182 AC: 1235 AN: 67764

Other (OTH) AF: 0.0105 AC: 22 AN: 2090

Alfa AF: 0.0158 Hom.: 6

Bravo AF: 0.0140

Asia WGS AF: 0.00781 AC: 27 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.6
DANN	Benign	0.52
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs34974495; hg19: chr18-58040789;