10-114054633-C-T

Position:

• chr10-114054633-C-T

Variant summary

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

The XR_007062383.1(LOC124902554):​n.194-7438G>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 0.429 in 151,844 control chromosomes in the GnomAD database, including 15,358 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 0.43 (15358 hom., cov: 31)
• Consequence: LOC124902554 XR_007062383.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899

Genes affected

LOC124902554 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902554	XR_007062383.1	n.194-7438G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65129 AN: 151726 Hom.: 15362 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.429 AC: 65140 AN: 151844 Hom.: 15358 Cov.: 31 AF XY: 0.436 AC XY: 32348 AN XY: 74178

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.432

Alfa AF: 0.491 Hom.: 24439

Bravo AF: 0.409

Asia WGS AF: 0.524 AC: 1822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10885531; hg19: chr10-115814392;