rs2595613

Variant names:

• chr8-92567026-C-A
• rs2595613
• ENST00000523284.3:n.544-1456G>T

Variant summary

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

The ENST00000523284.3(ENSG00000253634):​n.544-1456G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,084 control chromosomes in the GnomAD database, including 1,694 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 0.12 (1694 hom., cov: 32)
• Consequence: ENSG00000253634 ENST00000523284.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 1 publications found

Genes affected

ENSG00000253634 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724710	NR_125827.1	n.460-1456G>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253634	ENST00000523284.3	n.544-1456G>T		intron_variant	Intron 4 of 4	3
ENSG00000253634	ENST00000648652.1	n.534+1977G>T		intron_variant	Intron 4 of 13
ENSG00000253634	ENST00000653143.2	n.548-1456G>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17603 AN: 151966 Hom.: 1695 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0463

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0522

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.116 AC: 17617 AN: 152084 Hom.: 1694 Cov.: 32 AF XY: 0.115 AC XY: 8531 AN XY: 74356

African (AFR) AF: 0.257 AC: 10662 AN: 41476

American (AMR) AF: 0.148 AC: 2254 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0467 AC: 162 AN: 3472

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5174

South Asian (SAS) AF: 0.0460 AC: 222 AN: 4830

European-Finnish (FIN) AF: 0.0414 AC: 438 AN: 10592

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0522 AC: 3546 AN: 67970

Other (OTH) AF: 0.118 AC: 249 AN: 2104

Alfa AF: 0.0950 Hom.: 415

Bravo AF: 0.131

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.6
DANN	Benign	0.75
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2595613; hg19: chr8-93579254;