rs1525501

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000226965 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.0940

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.132

Alfa AF: 0.126 Hom.: 729

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1525501; hg19: chr7-109798853;