rs1597301

Variant names:

• chr8-92487589-T-C
• rs1597301
• ENST00000648652.1:n.1052+12167A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-92487589-T-C
• chr8-92487589-T-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000648652.1(ENSG00000253634):​n.1052+12167A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 152,052 control chromosomes in the GnomAD database, including 21,453 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 0.52 (21453 hom., cov: 32)
• Consequence: ENSG00000253634 ENST00000648652.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.727
• Publications: 4 publications found

Genes affected

ENSG00000253634 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375639	XR_007061005.1	n.425+13149A>G		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253634	ENST00000648652.1	n.1052+12167A>G		intron_variant	Intron 8 of 13
ENSG00000253634	ENST00000744168.1	n.397+13149A>G		intron_variant	Intron 4 of 6
ENSG00000253634	ENST00000744169.1	n.233+14771A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79511 AN: 151934 Hom.: 21439 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.523 AC: 79571 AN: 152052 Hom.: 21453 Cov.: 32 AF XY: 0.530 AC XY: 39379 AN XY: 74312

African (AFR) AF: 0.390 AC: 16183 AN: 41478

American (AMR) AF: 0.523 AC: 7991 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2051 AN: 3468

East Asian (EAS) AF: 0.484 AC: 2496 AN: 5156

South Asian (SAS) AF: 0.626 AC: 3018 AN: 4820

European-Finnish (FIN) AF: 0.637 AC: 6733 AN: 10570

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39224 AN: 67970

Other (OTH) AF: 0.531 AC: 1120 AN: 2110

Alfa AF: 0.557 Hom.: 103178

Bravo AF: 0.509

Asia WGS AF: 0.547 AC: 1899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	17
DANN	Benign	0.66
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs1597301; hg19: chr8-93499817;