rs11015839

Positions:

• chr10-18713958-G-A

Variant summary

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

The ENST00000654305.1(ENSG00000234244):​n.93+3597G>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 0.25 in 152,062 control chromosomes in the GnomAD database, including 4,868 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 0.25 (4868 hom., cov: 32)
• Consequence: ENST00000654305.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389

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 (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376440	XR_930721.2	n.68+3597G>A		intron_variant, non_coding_transcript_variant
LOC105376440	XR_930720.2	n.51+3597G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654305.1	n.93+3597G>A		intron_variant, non_coding_transcript_variant
	ENST00000654415.1	n.78+3597G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37934 AN: 151944 Hom.: 4866 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.250 AC: 37956 AN: 152062 Hom.: 4868 Cov.: 32 AF XY: 0.248 AC XY: 18469 AN XY: 74326

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.241

Alfa AF: 0.258 Hom.: 6223

Bravo AF: 0.257

Asia WGS AF: 0.302 AC: 1048 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	2.4
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11015839; hg19: chr10-19002887;