rs946553

Positions:

• chr10-93753053-C-T

Variant summary

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

The XR_246160.5(LOC101927013):​n.238-3069G>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 0.614 in 152,048 control chromosomes in the GnomAD database, including 29,101 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 0.61 (29101 hom., cov: 32)
• Consequence: LOC101927013 XR_246160.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551

Genes affected

LOC101927013 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927013	XR_246160.5	n.238-3069G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93321 AN: 151930 Hom.: 29090 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.614 AC: 93367 AN: 152048 Hom.: 29101 Cov.: 32 AF XY: 0.619 AC XY: 46009 AN XY: 74356

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.605

Alfa AF: 0.633 Hom.: 32399

Bravo AF: 0.608

Asia WGS AF: 0.762 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.54
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: rs946553; hg19: chr10-95512810;