rs2675677

Positions:

• chr10-73888491-C-A
• chr10-73888491-C-T

Variant summary

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

The XR_007062196.1(LOC124902454):​n.416G>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 0.715 in 151,986 control chromosomes in the GnomAD database, including 39,505 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 0.71 (39505 hom., cov: 32)
• Consequence: LOC124902454 XR_007062196.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

Genes affected

LOC124902454 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902454	XR_007062196.1	n.416G>T		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108597 AN: 151868 Hom.: 39479 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.715 AC: 108657 AN: 151986 Hom.: 39505 Cov.: 32 AF XY: 0.706 AC XY: 52380 AN XY: 74238

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.754

Alfa AF: 0.744 Hom.: 83047

Bravo AF: 0.717

Asia WGS AF: 0.508 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	15
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2675677; hg19: chr10-75648249;