6-14802456-C-T

Position:

• chr6-14802456-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000629853.2(ENSG00000234261):​n.205-12358G>A variant causes a intron, non coding transcript 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: ENST00000629853.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000629853.2	n.205-12358G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.0933

Gnomad4 ASJ AF: 0.0315

Gnomad4 EAS AF: 0.0178

Gnomad4 SAS AF: 0.0960

Gnomad4 FIN AF: 0.0185

Gnomad4 NFE AF: 0.0287

Gnomad4 OTH AF: 0.0809

Alfa AF: 0.0420 Hom.: 478

Bravo AF: 0.124

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs233492; hg19: chr6-14802687;