rs1943217

Positions:

• chr18-60376948-T-G

Variant summary

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

The ENST00000658928.1(ENSG00000285681):​n.156+47603T>G 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 0.395 in 151,976 control chromosomes in the GnomAD database, including 14,182 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 0.40 (14182 hom., cov: 32)
• Consequence: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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 (AFR) allele frequency at 95% confidence interval = 0.65 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+47603T>G		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.113+47603T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59975 AN: 151858 Hom.: 14152 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.395 AC: 60051 AN: 151976 Hom.: 14182 Cov.: 32 AF XY: 0.387 AC XY: 28762 AN XY: 74288

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.358

Alfa AF: 0.360 Hom.: 3340

Bravo AF: 0.417

Asia WGS AF: 0.247 AC: 860 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	0.86
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1943217; hg19: chr18-58044181;