6-31272654-G-T

Variant names:

• chr6-31272654-G-T
• rs2074488
• ENST00000692808.1:n.*64G>T

Variant summary

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

The ENST00000692808.1(ENSG00000288813):​n.*64G>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,212 control chromosomes in the GnomAD database, including 1,423 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 0.13 (1423 hom., cov: 33)
• Consequence: ENSG00000288813 ENST00000692808.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.705

Genes affected

ENSG00000288813 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288813	ENST00000692808.1	n.*64G>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19320 AN: 152094 Hom.: 1419 Cov.: 33

Gnomad AFR AF: 0.0906

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.0729

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.0886

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

GnomAD4 genome AF: 0.127 AC: 19331 AN: 152212 Hom.: 1423 Cov.: 33 AF XY: 0.130 AC XY: 9688 AN XY: 74418

Gnomad4 AFR AF: 0.0904

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.0730

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.0886

Alfa AF: 0.121 Hom.: 105

Bravo AF: 0.120

Asia WGS AF: 0.149 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2074488; hg19: chr6-31240431;