10-73889290-G-A

Position:

• chr10-73889290-G-A

Variant summary

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

The XR_007062196.1(LOC124902454):​n.174C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,084 control chromosomes in the GnomAD database, including 40,423 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 0.72 (40423 hom., cov: 31)
• Consequence: LOC124902454 XR_007062196.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

Genes affected

LOC124902454 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902454	XR_007062196.1	n.174C>T		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109897 AN: 151968 Hom.: 40400 Cov.: 31

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.723 AC: 109953 AN: 152084 Hom.: 40423 Cov.: 31 AF XY: 0.713 AC XY: 53037 AN XY: 74358

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.767

Alfa AF: 0.739 Hom.: 6965

Bravo AF: 0.724

Asia WGS AF: 0.518 AC: 1805 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2675675; hg19: chr10-75649048;