rs17773774

Positions:

• chr18-60392893-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000658928.1(ENSG00000285681):​n.156+63548C>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 0.132 in 151,874 control chromosomes in the GnomAD database, including 1,753 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 0.13 (1753 hom., cov: 32)
• Consequence: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658928.1	n.156+63548C>A		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.113+63548C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20081 AN: 151758 Hom.: 1752 Cov.: 32

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0373

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.132 AC: 20073 AN: 151874 Hom.: 1753 Cov.: 32 AF XY: 0.128 AC XY: 9513 AN XY: 74240

Gnomad4 AFR AF: 0.0339

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0376

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.128

Alfa AF: 0.176 Hom.: 2252

Bravo AF: 0.126

Asia WGS AF: 0.0810 AC: 281 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	14
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17773774; hg19: chr18-58060126;