chr6-167141288-G-C

Variant names:

• chr6-167141288-G-C
• rs367523
• XR_002956379.2:n.64C>G

Variant summary

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

The XR_002956379.2(LOC112267970):​n.64C>G 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 0.63 in 152,056 control chromosomes in the GnomAD database, including 30,367 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 0.63 (30367 hom., cov: 32)
• Consequence: LOC112267970 XR_002956379.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 5 publications found

Genes affected

LOC112267970 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832763.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308245	ENST00000832763.1		n.-97C>G		upstream_gene	N/A
	ENSG00000308245	ENST00000832764.1		n.-60C>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95742 AN: 151938 Hom.: 30359 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.630 AC: 95794 AN: 152056 Hom.: 30367 Cov.: 32 AF XY: 0.628 AC XY: 46650 AN XY: 74326

African (AFR) AF: 0.611 AC: 25311 AN: 41440

American (AMR) AF: 0.737 AC: 11261 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2142 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2734 AN: 5178

South Asian (SAS) AF: 0.601 AC: 2896 AN: 4816

European-Finnish (FIN) AF: 0.591 AC: 6249 AN: 10576

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43288 AN: 67974

Other (OTH) AF: 0.640 AC: 1354 AN: 2116

Alfa AF: 0.639 Hom.: 3896

Bravo AF: 0.636

Asia WGS AF: 0.595 AC: 2069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.67
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs367523; hg19: chr6-167554776; COSMIC: COSV59474868;