6-14802456-C-T

Variant names:

• chr6-14802456-C-T
• rs233492
• ENST00000629853.3:n.205-12358G>A

Variant summary

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

The ENST00000629853.3(ENSG00000234261):​n.205-12358G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,130 control chromosomes in the GnomAD database, including 2,031 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 0.11 (2031 hom., cov: 32)
• Consequence: ENSG00000234261 ENST00000629853.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47
• Publications: 3 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000629853.3. 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	ENST00000629853.3	TSL:5	n.205-12358G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16766 AN: 152012 Hom.: 2016 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.0315

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.0185

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0287

Gnomad OTH AF: 0.0822

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

GnomAD4 genome AF: 0.111 AC: 16829 AN: 152130 Hom.: 2031 Cov.: 32 AF XY: 0.108 AC XY: 8031 AN XY: 74384

African (AFR) AF: 0.298 AC: 12357 AN: 41452

American (AMR) AF: 0.0933 AC: 1427 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0315 AC: 109 AN: 3464

East Asian (EAS) AF: 0.0178 AC: 92 AN: 5176

South Asian (SAS) AF: 0.0960 AC: 463 AN: 4824

European-Finnish (FIN) AF: 0.0185 AC: 196 AN: 10596

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0287 AC: 1950 AN: 68010

Other (OTH) AF: 0.0809 AC: 171 AN: 2114

Alfa AF: 0.0498 Hom.: 956

Bravo AF: 0.124

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.55
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs233492; hg19: chr6-14802687;