6-14988536-T-C

Variant names:

• chr6-14988536-T-C
• rs2327869
• ENST00000437648.1:n.486+8880A>G

Variant summary

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

The ENST00000653525.1(ENSG00000234261):​n.397+8880A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,916 control chromosomes in the GnomAD database, including 13,246 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 0.40 (13246 hom., cov: 31)
• Consequence: ENSG00000234261 ENST00000653525.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653525.1. 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	ENST00000437648.1	TSL:5	n.486+8880A>G		intron	N/A
	ENSG00000234261	ENST00000629853.3	TSL:5	n.204+8880A>G		intron	N/A
	ENSG00000234261	ENST00000653525.1		n.397+8880A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59980 AN: 151796 Hom.: 13204 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.395 AC: 60082 AN: 151916 Hom.: 13246 Cov.: 31 AF XY: 0.398 AC XY: 29556 AN XY: 74260

African (AFR) AF: 0.597 AC: 24709 AN: 41386

American (AMR) AF: 0.351 AC: 5349 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1407 AN: 3472

East Asian (EAS) AF: 0.330 AC: 1705 AN: 5166

South Asian (SAS) AF: 0.597 AC: 2865 AN: 4802

European-Finnish (FIN) AF: 0.297 AC: 3142 AN: 10568

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.289 AC: 19622 AN: 67968

Other (OTH) AF: 0.377 AC: 795 AN: 2110

Alfa AF: 0.328 Hom.: 29350

Bravo AF: 0.400

Asia WGS AF: 0.491 AC: 1706 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	0.33
DANN	Benign	0.49
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2327869; hg19: chr6-14988767;