rs10454657

Positions:

• chr13-75017686-C-T

Variant summary

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

The XR_001749918.1(LOC107984620):​n.208+4827G>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 0.479 in 151,736 control chromosomes in the GnomAD database, including 19,212 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 0.48 (19212 hom., cov: 31)
• Consequence: LOC107984620 XR_001749918.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

LOC107984620 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984620	XR_001749918.1	n.208+4827G>A		intron_variant, non_coding_transcript_variant
LOC107984620	XR_001749917.1	n.257+4827G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72743 AN: 151618 Hom.: 19216 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.479 AC: 72743 AN: 151736 Hom.: 19212 Cov.: 31 AF XY: 0.479 AC XY: 35470 AN XY: 74114

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.508

Alfa AF: 0.560 Hom.: 50867

Bravo AF: 0.470

Asia WGS AF: 0.502 AC: 1741 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.076
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10454657; hg19: chr13-75591823;