rs1525501

Variant names:

• chr7-110158796-G-A
• rs1525501
• ENST00000658032.1:n.438+22182C>T

Variant summary

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

The ENST00000658032.1(ENSG00000226965):​n.438+22182C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,142 control chromosomes in the GnomAD database, including 1,896 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 0.14 (1896 hom., cov: 32)
• Consequence: ENSG00000226965 ENST00000658032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 6 publications found

Genes affected

ENSG00000226965 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.422 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
ENSG00000226965	ENST00000658032.1	n.438+22182C>T		intron_variant	Intron 5 of 5
ENSG00000226965	ENST00000667232.1	n.519+22182C>T		intron_variant	Intron 6 of 7
ENSG00000226965	ENST00000755897.1	n.33+22182C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21015 AN: 152024 Hom.: 1892 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.0940

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.138 AC: 21027 AN: 152142 Hom.: 1896 Cov.: 32 AF XY: 0.143 AC XY: 10610 AN XY: 74368

African (AFR) AF: 0.148 AC: 6131 AN: 41514

American (AMR) AF: 0.125 AC: 1904 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 611 AN: 3470

East Asian (EAS) AF: 0.437 AC: 2253 AN: 5156

South Asian (SAS) AF: 0.318 AC: 1529 AN: 4812

European-Finnish (FIN) AF: 0.0940 AC: 995 AN: 10590

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.106 AC: 7195 AN: 68006

Other (OTH) AF: 0.132 AC: 278 AN: 2110

Alfa AF: 0.126 Hom.: 797

Bravo AF: 0.139

Asia WGS AF: 0.366 AC: 1269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.80
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs1525501; hg19: chr7-109798853;