rs10002

Positions:

• chr6-151393970-G-A

Variant summary

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

The XM_047419613.1(LOC124901232):​c.*2366G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,672 control chromosomes in the GnomAD database, including 12,908 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 0.37 (12908 hom., cov: 30)
• Consequence: LOC124901232 XM_047419613.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

Genes affected

LOC124901232 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901232	XM_047419613.1	c.*2366G>A		3_prime_UTR_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56664 AN: 151554 Hom.: 12878 Cov.: 30

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.374 AC: 56749 AN: 151672 Hom.: 12908 Cov.: 30 AF XY: 0.377 AC XY: 27944 AN XY: 74098

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.363

Alfa AF: 0.265 Hom.: 4999

Bravo AF: 0.395

Asia WGS AF: 0.551 AC: 1912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.43
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10002; hg19: chr6-151715105;