rs10483532

Positions:

• chr14-39669396-T-G

Variant summary

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

The ENST00000652126.1(ENSG00000258526):​n.457+13588T>G 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 0.0236 in 152,246 control chromosomes in the GnomAD database, including 129 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 0.024 (129 hom., cov: 32)
• Consequence: ENST00000652126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370461	XR_001750723.2	n.567+13588T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652126.1	n.457+13588T>G		intron_variant, non_coding_transcript_variant
	ENST00000650911.1	n.417+13588T>G		intron_variant, non_coding_transcript_variant
	ENST00000651829.1	n.1196+13588T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0236 AC: 3585 AN: 152130 Hom.: 127 Cov.: 32

Gnomad AFR AF: 0.00504

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.0767

Gnomad SAS AF: 0.0602

Gnomad FIN AF: 0.0193

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0120

Gnomad OTH AF: 0.0353

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

GnomAD4 genome AF: 0.0236 AC: 3600 AN: 152246 Hom.: 129 Cov.: 32 AF XY: 0.0263 AC XY: 1958 AN XY: 74436

Gnomad4 AFR AF: 0.00503

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.0771

Gnomad4 SAS AF: 0.0602

Gnomad4 FIN AF: 0.0193

Gnomad4 NFE AF: 0.0120

Gnomad4 OTH AF: 0.0373

Alfa AF: 0.0207 Hom.: 149

Bravo AF: 0.0300

Asia WGS AF: 0.104 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.7
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483532; hg19: chr14-40138600;