rs641525

Variant names:

• chr8-2882980-T-G
• rs641525
• ENST00000725259.1:n.1167-42785T>G

Variant summary

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

The ENST00000725259.1(ENSG00000253853):​n.1167-42785T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,170 control chromosomes in the GnomAD database, including 3,873 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 0.17 (3873 hom., cov: 32)
• Consequence: ENSG00000253853 ENST00000725259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 7 publications found

Genes affected

ENSG00000253853 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377785	NR_168441.1	n.1166+45216T>G		intron_variant	Intron 6 of 11
LOC105377785	NR_168442.1	n.1331-33355T>G		intron_variant	Intron 7 of 14
LOC105377785	NR_168443.1	n.1171+45216T>G		intron_variant	Intron 6 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253853	ENST00000725259.1	n.1167-42785T>G		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25700 AN: 152052 Hom.: 3871 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.0302

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0570

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.169 AC: 25744 AN: 152170 Hom.: 3873 Cov.: 32 AF XY: 0.168 AC XY: 12533 AN XY: 74428

African (AFR) AF: 0.391 AC: 16218 AN: 41470

American (AMR) AF: 0.115 AC: 1758 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1675 AN: 5158

South Asian (SAS) AF: 0.230 AC: 1112 AN: 4826

European-Finnish (FIN) AF: 0.0302 AC: 321 AN: 10624

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.0571 AC: 3881 AN: 68020

Other (OTH) AF: 0.176 AC: 370 AN: 2108

Alfa AF: 0.0986 Hom.: 5505

Bravo AF: 0.185

Asia WGS AF: 0.296 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.55
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs641525; hg19: chr8-2740502;