rs931078

Positions:

• chr18-60715469-C-G

Variant summary

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

The ENST00000655645.1(ENSG00000267098):​n.164+15417G>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 0.445 in 151,834 control chromosomes in the GnomAD database, including 16,243 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 0.45 (16243 hom., cov: 31)
• Consequence: ENST00000655645.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 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
	ENST00000655645.1	n.164+15417G>C		intron_variant, non_coding_transcript_variant
	ENST00000591869.1	n.228+15417G>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67600 AN: 151716 Hom.: 16236 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.445 AC: 67631 AN: 151834 Hom.: 16243 Cov.: 31 AF XY: 0.448 AC XY: 33251 AN XY: 74214

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.488

Alfa AF: 0.471 Hom.: 2206

Bravo AF: 0.435

Asia WGS AF: 0.599 AC: 2084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs931078; hg19: chr18-58382702;