rs10483517

Positions:

• chr14-39755707-A-T

Variant summary

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

The ENST00000652126.1(ENSG00000258526):​n.457+99899A>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 0.174 in 151,996 control chromosomes in the GnomAD database, including 2,537 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 (2537 hom., cov: 32)
• Consequence: ENST00000652126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370461	XR_007064121.1	n.11935+32357A>T		intron_variant, non_coding_transcript_variant
LOC105370461	XR_007064127.1	n.453-99180A>T		intron_variant, non_coding_transcript_variant
LOC105370461	XR_007064128.1	n.453-5957A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000652126.1	n.457+99899A>T		intron_variant, non_coding_transcript_variant
	ENST00000650911.1	n.417+99899A>T		intron_variant, non_coding_transcript_variant
	ENST00000651829.1	n.1323+43600A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26488 AN: 151878 Hom.: 2541 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.174 AC: 26483 AN: 151996 Hom.: 2537 Cov.: 32 AF XY: 0.177 AC XY: 13155 AN XY: 74280

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.158

Alfa AF: 0.163 Hom.: 243

Bravo AF: 0.175

Asia WGS AF: 0.232 AC: 808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.59
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483517; hg19: chr14-40224911;