6-14633142-A-G

Variant names:

• chr6-14633142-A-G
• rs860751
• ENST00000702111.1:n.156+10809T>C

Variant summary

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

The ENST00000702111.1(ENSG00000234261):​n.156+10809T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,222 control chromosomes in the GnomAD database, including 48,100 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 0.75 (48100 hom., cov: 32)
• Consequence: ENSG00000234261 ENST00000702111.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 5 publications found

Genes affected

ENSG00000234261 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702111.1. 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	ENST00000702111.1		n.156+10809T>C		intron	N/A
	ENSG00000234261	ENST00000729738.1		n.229+10809T>C		intron	N/A
	ENSG00000234261	ENST00000729739.1		n.165+10809T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114468 AN: 152104 Hom.: 48104 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.752 AC: 114494 AN: 152222 Hom.: 48100 Cov.: 32 AF XY: 0.758 AC XY: 56389 AN XY: 74428

African (AFR) AF: 0.345 AC: 14328 AN: 41476

American (AMR) AF: 0.832 AC: 12729 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2955 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5166 AN: 5182

South Asian (SAS) AF: 0.856 AC: 4128 AN: 4822

European-Finnish (FIN) AF: 0.949 AC: 10073 AN: 10616

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62351 AN: 68026

Other (OTH) AF: 0.785 AC: 1660 AN: 2114

Alfa AF: 0.714 Hom.: 20000

Bravo AF: 0.727

Asia WGS AF: 0.883 AC: 3071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.44
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs860751; hg19: chr6-14633373;