rs11015939

Positions:

• chr10-18729013-G-A

Variant summary

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

The ENST00000654305.1(ENSG00000234244):​n.94-17676G>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 0.17 in 151,952 control chromosomes in the GnomAD database, including 2,379 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 0.17 (2379 hom., cov: 31)
• Consequence: ENST00000654305.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376440	XR_930721.2	n.69-17676G>A		intron_variant, non_coding_transcript_variant
LOC105376440	XR_930720.2	n.51+18652G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654305.1	n.94-17676G>A		intron_variant, non_coding_transcript_variant
	ENST00000654415.1	n.79-3403G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25839 AN: 151834 Hom.: 2377 Cov.: 31

Gnomad AFR AF: 0.0967

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.170 AC: 25851 AN: 151952 Hom.: 2379 Cov.: 31 AF XY: 0.170 AC XY: 12591 AN XY: 74272

Gnomad4 AFR AF: 0.0966

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.165

Alfa AF: 0.195 Hom.: 1386

Bravo AF: 0.165

Asia WGS AF: 0.182 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.86
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11015939; hg19: chr10-19017942;