rs1145625

Variant names:

• chr5-158225073-A-G
• rs1145625
• ENST00000809623.1:n.178-25917A>G

Variant summary

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

The ENST00000809623.1(ENSG00000253673):​n.178-25917A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,964 control chromosomes in the GnomAD database, including 1,976 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 0.16 (1976 hom., cov: 31)
• Consequence: ENSG00000253673 ENST00000809623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345
• Publications: 2 publications found

Genes affected

ENSG00000253673 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.243 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
ENSG00000253673	ENST00000809623.1	n.178-25917A>G		intron_variant	Intron 1 of 1
ENSG00000253673	ENST00000809624.1	n.141+18825A>G		intron_variant	Intron 2 of 3
ENSG00000253673	ENST00000809625.1	n.39-16295A>G		intron_variant	Intron 1 of 1
ENSG00000253673	ENST00000809626.1	n.104-25917A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23974 AN: 151844 Hom.: 1971 Cov.: 31

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.158 AC: 23997 AN: 151964 Hom.: 1976 Cov.: 31 AF XY: 0.162 AC XY: 12006 AN XY: 74266

African (AFR) AF: 0.182 AC: 7524 AN: 41436

American (AMR) AF: 0.123 AC: 1885 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 460 AN: 3472

East Asian (EAS) AF: 0.219 AC: 1126 AN: 5150

South Asian (SAS) AF: 0.255 AC: 1227 AN: 4818

European-Finnish (FIN) AF: 0.163 AC: 1721 AN: 10552

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9503 AN: 67948

Other (OTH) AF: 0.164 AC: 345 AN: 2110

Alfa AF: 0.145 Hom.: 7002

Bravo AF: 0.151

Asia WGS AF: 0.288 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.73
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1145625; hg19: chr5-157652081;