rs582970

Variant names:

• chr18-60497226-T-C
• rs582970
• ENST00000650201.1:n.215+17554T>C

Your query was ambiguous. Multiple possible variants found:

• chr18-60497226-T-C
• chr18-60497226-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650201.1(ENSG00000285681):​n.215+17554T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,004 control chromosomes in the GnomAD database, including 14,099 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 0.43 (14099 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 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
ENSG00000285681	ENST00000650201.1	n.215+17554T>C		intron_variant	Intron 2 of 3
ENSG00000285681	ENST00000658928.1	n.258+17554T>C		intron_variant	Intron 2 of 3
ENSG00000285681	ENST00000667405.1	n.128+17554T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64611 AN: 151886 Hom.: 14077 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.425 AC: 64676 AN: 152004 Hom.: 14099 Cov.: 32 AF XY: 0.425 AC XY: 31587 AN XY: 74288

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.398

Alfa AF: 0.308 Hom.: 947

Bravo AF: 0.420

Asia WGS AF: 0.412 AC: 1431 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs582970; hg19: chr18-58164459;