6-14596134-A-G

Variant names:

• chr6-14596134-A-G
• rs6914079
• XR_001743992.2:n.1827T>C

Variant summary

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

The XR_241980.4(LOC101928354):​n.1689T>C 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 0.829 in 152,148 control chromosomes in the GnomAD database, including 52,342 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 0.83 (52342 hom., cov: 32)
• Consequence: LOC101928354 XR_241980.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 9 publications found

Genes affected

LOC101928354 (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 (SAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729738.1. 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
	ENSG00000234261	ENST00000729738.1		n.373+1380T>C		intron	N/A
	ENSG00000234261	ENST00000729739.1		n.309+1380T>C		intron	N/A
	ENSG00000234261	ENST00000729740.1		n.270+1380T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126035 AN: 152030 Hom.: 52298 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.829 AC: 126127 AN: 152148 Hom.: 52342 Cov.: 32 AF XY: 0.827 AC XY: 61519 AN XY: 74356

African (AFR) AF: 0.858 AC: 35612 AN: 41514

American (AMR) AF: 0.795 AC: 12142 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.852 AC: 2956 AN: 3470

East Asian (EAS) AF: 0.747 AC: 3852 AN: 5160

South Asian (SAS) AF: 0.860 AC: 4144 AN: 4816

European-Finnish (FIN) AF: 0.786 AC: 8325 AN: 10594

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56283 AN: 68008

Other (OTH) AF: 0.853 AC: 1794 AN: 2102

Alfa AF: 0.824 Hom.: 161598

Bravo AF: 0.826

Asia WGS AF: 0.801 AC: 2780 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.65
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs6914079; hg19: chr6-14596365;