10-114047257-C-T

Position:

• chr10-114047257-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.194-62G>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 0.622 in 149,880 control chromosomes in the GnomAD database, including 29,298 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 0.62 (29298 hom., cov: 27)
• Consequence: LOC124902554 XR_007062383.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

Genes affected

LOC124902554 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902554	XR_007062383.1	n.194-62G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.622 AC: 93124 AN: 149770 Hom.: 29264 Cov.: 27

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.622 AC: 93208 AN: 149880 Hom.: 29298 Cov.: 27 AF XY: 0.629 AC XY: 45894 AN XY: 72918

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.603

Alfa AF: 0.632 Hom.: 40465

Bravo AF: 0.611

Asia WGS AF: 0.689 AC: 2393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3813720; hg19: chr10-115807016;