rs10002

Variant names:

• chr6-151393970-G-A
• rs10002
• XM_047419613.1:c.*2366G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000748755.1(ENSG00000297539):​n.206C>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 0.374 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: ENSG00000297539 ENST00000748755.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 6 publications found

Genes affected

LOC124901232 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748755.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297539	ENST00000748755.1		n.206C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000297539	ENST00000748756.1		n.205C>T		non_coding_transcript_exon	Exon 1 of 2

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

African (AFR) AF: 0.614 AC: 25383 AN: 41314

American (AMR) AF: 0.354 AC: 5384 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1040 AN: 3464

East Asian (EAS) AF: 0.689 AC: 3540 AN: 5136

South Asian (SAS) AF: 0.381 AC: 1837 AN: 4816

European-Finnish (FIN) AF: 0.252 AC: 2644 AN: 10512

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15798 AN: 67896

Other (OTH) AF: 0.363 AC: 763 AN: 2100

Alfa AF: 0.283 Hom.: 7799

Bravo AF: 0.395

Asia WGS AF: 0.551 AC: 1912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.43
DANN	Benign	0.33
PhyloP100		-2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10002;

hg19: chr6-151715105;