5-57956140-T-G

Variant names:

• chr5-57956140-T-G
• rs1027164
• ENST00000761558.1:n.149-19040T>G

Variant summary

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

The ENST00000761558.1(ENSG00000299201):​n.149-19040T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 151,864 control chromosomes in the GnomAD database, including 33,772 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 0.66 (33772 hom., cov: 31)
• Consequence: ENSG00000299201 ENST00000761558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 1 publications found

Genes affected

ENSG00000299201 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.727 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
ENSG00000299201	ENST00000761558.1	n.149-19040T>G		intron_variant	Intron 2 of 3
ENSG00000299201	ENST00000761559.1	n.123-19040T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100876 AN: 151744 Hom.: 33757 Cov.: 31

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.665 AC: 100940 AN: 151864 Hom.: 33772 Cov.: 31 AF XY: 0.669 AC XY: 49622 AN XY: 74210

African (AFR) AF: 0.624 AC: 25835 AN: 41428

American (AMR) AF: 0.738 AC: 11248 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2394 AN: 3466

East Asian (EAS) AF: 0.649 AC: 3314 AN: 5106

South Asian (SAS) AF: 0.687 AC: 3304 AN: 4810

European-Finnish (FIN) AF: 0.721 AC: 7617 AN: 10568

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45092 AN: 67936

Other (OTH) AF: 0.646 AC: 1361 AN: 2106

Alfa AF: 0.629 Hom.: 3336

Bravo AF: 0.663

Asia WGS AF: 0.665 AC: 2310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.70
DANN	Benign	0.56
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1027164; hg19: chr5-57251967;