chr6-14429331-T-C

Variant names:

• chr6-14429331-T-C
• rs12662871
• XR_007059468.1:n.3166A>G

Variant summary

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

The XR_007059468.1(LOC105374942):​n.3166A>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 0.187 in 151,910 control chromosomes in the GnomAD database, including 2,732 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 0.19 (2732 hom., cov: 32)
• Consequence: LOC105374942 XR_007059468.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 4 publications found

Genes affected

LOC105374942 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729876.1. 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
	ENSG00000286277	ENST00000729876.1		n.238-2449T>C		intron	N/A
	ENSG00000286277	ENST00000729877.1		n.51-27644T>C		intron	N/A
	ENSG00000286277	ENST00000729878.1		n.51-2449T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28362 AN: 151792 Hom.: 2730 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.187 AC: 28389 AN: 151910 Hom.: 2732 Cov.: 32 AF XY: 0.184 AC XY: 13661 AN XY: 74234

African (AFR) AF: 0.240 AC: 9942 AN: 41400

American (AMR) AF: 0.126 AC: 1918 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 754 AN: 3472

East Asian (EAS) AF: 0.168 AC: 865 AN: 5160

South Asian (SAS) AF: 0.206 AC: 993 AN: 4814

European-Finnish (FIN) AF: 0.146 AC: 1535 AN: 10542

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11766 AN: 67934

Other (OTH) AF: 0.179 AC: 377 AN: 2106

Alfa AF: 0.177 Hom.: 10593

Bravo AF: 0.185

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.76
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs12662871; hg19: chr6-14429562;