chr5-159391737-A-C

Variant names:

• chr5-159391737-A-C
• rs6556416
• ENST00000635333.1:n.283-796A>C

Variant summary

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

The ENST00000635333.1(ENSG00000249738):​n.283-796A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 151,874 control chromosomes in the GnomAD database, including 43,557 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 0.75 (43557 hom., cov: 31)
• Consequence: ENSG00000249738 ENST00000635333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 40 publications found

Genes affected

ENSG00000249738 (HGNC:58156):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 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
ENSG00000249738	ENST00000635333.1	n.283-796A>C		intron_variant	Intron 3 of 7	5
ENSG00000249738	ENST00000641150.1	n.533-24787A>C		intron_variant	Intron 4 of 4
ENSG00000249738	ENST00000648969.1	n.54-24787A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114471 AN: 151758 Hom.: 43501 Cov.: 31

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.754 AC: 114589 AN: 151874 Hom.: 43557 Cov.: 31 AF XY: 0.762 AC XY: 56585 AN XY: 74210

African (AFR) AF: 0.830 AC: 34381 AN: 41404

American (AMR) AF: 0.794 AC: 12111 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2164 AN: 3466

East Asian (EAS) AF: 0.899 AC: 4637 AN: 5160

South Asian (SAS) AF: 0.832 AC: 4003 AN: 4814

European-Finnish (FIN) AF: 0.769 AC: 8095 AN: 10526

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.689 AC: 46791 AN: 67932

Other (OTH) AF: 0.745 AC: 1571 AN: 2108

Alfa AF: 0.711 Hom.: 16406

Bravo AF: 0.758

Asia WGS AF: 0.874 AC: 3027 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.70
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs6556416; hg19: chr5-158818745;