chr6-14475296-A-T

Position:

• chr6-14475296-A-T

Variant summary

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

The ENST00000666857.1(ENSG00000286277):​n.393-22761A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 152,048 control chromosomes in the GnomAD database, including 20,088 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 0.50 (20088 hom., cov: 32)
• Consequence: ENSG00000286277 ENST00000666857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

ENSG00000286277 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928331	XR_001743994.3	n.296-22761A>T		intron_variant
LOC101928331	XR_001743995.3	n.338+695A>T		intron_variant
LOC101928331	XR_001743996.3	n.338+695A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286277	ENST00000666857.1	n.393-22761A>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76333 AN: 151930 Hom.: 20053 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.503 AC: 76435 AN: 152048 Hom.: 20088 Cov.: 32 AF XY: 0.504 AC XY: 37449 AN XY: 74330

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.478

Alfa AF: 0.462 Hom.: 2185

Bravo AF: 0.518

Asia WGS AF: 0.674 AC: 2340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3761987; hg19: chr6-14475527;