rs12602978

Positions:

• chr17-27240054-C-T

Variant summary

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

The ENST00000581944.1(ENSG00000265246):​n.49+1559G>A 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 0.0953 in 152,202 control chromosomes in the GnomAD database, including 1,247 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 0.095 (1247 hom., cov: 32)
• Consequence: ENST00000581944.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903956	XR_007065676.1	n.97+1559G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000581944.1	n.49+1559G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0952 AC: 14479 AN: 152086 Hom.: 1234 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.0433

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0253

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0330

Gnomad OTH AF: 0.0794

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

GnomAD4 genome AF: 0.0953 AC: 14506 AN: 152202 Hom.: 1247 Cov.: 32 AF XY: 0.0980 AC XY: 7292 AN XY: 74398

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.0850

Gnomad4 ASJ AF: 0.0433

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0253

Gnomad4 NFE AF: 0.0330

Gnomad4 OTH AF: 0.0862

Alfa AF: 0.0507 Hom.: 163

Bravo AF: 0.102

Asia WGS AF: 0.239 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12602978; hg19: chr17-25567080;