rs10502411

Positions:

• chr18-11373581-G-A
• chr18-11373581-G-T

Variant summary

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

The ENST00000592198.1(ENSG00000267051):​n.155+4674C>T 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 0.0818 in 152,230 control chromosomes in the GnomAD database, including 1,161 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 0.082 (1161 hom., cov: 32)
• Consequence: ENST00000592198.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985173	XR_007066289.1	n.614-4929C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000592198.1	n.155+4674C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12450 AN: 152112 Hom.: 1164 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0662

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0494

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0818 AC: 12455 AN: 152230 Hom.: 1161 Cov.: 32 AF XY: 0.0896 AC XY: 6668 AN XY: 74446

Gnomad4 AFR AF: 0.0371

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.0662

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0494

Gnomad4 OTH AF: 0.0847

Alfa AF: 0.0661 Hom.: 79

Bravo AF: 0.0875

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.23
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502411; hg19: chr18-11373580;