rs476941

Positions:

• chr18-2111077-C-T

Variant summary

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

The ENST00000639316.2(ENSG00000263745):​n.619+15123G>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 0.697 in 151,982 control chromosomes in the GnomAD database, including 36,942 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 0.70 (36942 hom., cov: 31)
• Consequence: ENST00000639316.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371956	XR_935087.3	n.271+567G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000639316.2	n.619+15123G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105902 AN: 151864 Hom.: 36921 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.697 AC: 105980 AN: 151982 Hom.: 36942 Cov.: 31 AF XY: 0.698 AC XY: 51890 AN XY: 74314

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.679

Alfa AF: 0.688 Hom.: 32775

Bravo AF: 0.688

Asia WGS AF: 0.687 AC: 2390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.29
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs476941; hg19: chr18-2111078;