rs7227255

chr18-60388498-G-Achr18-60388498-G-Cchr18-60388498-G-T

Variant summary

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

The ENST00000658928.1(ENSG00000285681):n.156+59153G>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 0.0837 in 152,060 control chromosomes in the GnomAD database, including 1,352 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 0.084 (1352 hom., cov: 32)
• Consequence: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 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+59153G>A		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.113+59153G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0835 AC: 12693 AN: 151942 Hom.: 1345 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0345

Gnomad FIN AF: 0.0119

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0193

Gnomad OTH AF: 0.0549

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

GnomAD4 genome AF: 0.0837 AC: 12724 AN: 152060 Hom.: 1352 Cov.: 32 AF XY: 0.0807 AC XY: 6002 AN XY: 74340

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.0284

Gnomad4 ASJ AF: 0.00346

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0337

Gnomad4 FIN AF: 0.0119

Gnomad4 NFE AF: 0.0193

Gnomad4 OTH AF: 0.0543

Alfa AF: 0.0272 Hom.: 84

Bravo AF: 0.0921

Asia WGS AF: 0.0240 AC: 82 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.9
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7227255; hg19: chr18-58055731;