rs1033772

Positions:

• chr10-113486173-G-A
• chr10-113486173-G-C

Variant summary

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

The ENST00000658845.1(ENSG00000286289):​n.63-556C>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 0.416 in 151,896 control chromosomes in the GnomAD database, including 13,889 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 0.42 (13889 hom., cov: 32)
• Consequence: ENST00000658845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984270	XR_001747591.2	n.338-556C>T		intron_variant, non_coding_transcript_variant
LOC107984270	XR_001747592.2	n.814+524C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000658845.1	n.63-556C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63163 AN: 151778 Hom.: 13867 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.416 AC: 63223 AN: 151896 Hom.: 13889 Cov.: 32 AF XY: 0.423 AC XY: 31442 AN XY: 74250

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.450

Alfa AF: 0.364 Hom.: 17383

Bravo AF: 0.435

Asia WGS AF: 0.585 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	10
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1033772; hg19: chr10-115245932;