rs582970

Positions:

• 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 ENST00000658928.1(ENSG00000285681):​n.258+17554T>C variant causes a intron, non coding transcript 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: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000658928.1	n.258+17554T>C		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.215+17554T>C		intron_variant, non_coding_transcript_variant
	ENST00000667405.1	n.128+17554T>C		intron_variant, non_coding_transcript_variant

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;