6-31272654-G-T

Variant names:

• chr6-31272654-G-T
• rs2074488
• ENST00000692808.2:n.1259G>T

Variant summary

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

The ENST00000692808.2(ENSG00000288813):​n.1259G>T variant causes a non coding transcript exon 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 ENST00000692808.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.705
• Publications: 55 publications found

Genes affected

ENSG00000288813 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692808.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288813	ENST00000692808.2		n.1259G>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298396	ENST00000755297.1		n.32+1548G>T		intron	N/A

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

African (AFR) AF: 0.0904 AC: 3757 AN: 41546

American (AMR) AF: 0.139 AC: 2126 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0216 AC: 75 AN: 3470

East Asian (EAS) AF: 0.245 AC: 1269 AN: 5170

South Asian (SAS) AF: 0.0730 AC: 352 AN: 4824

European-Finnish (FIN) AF: 0.206 AC: 2178 AN: 10594

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9309 AN: 67998

Other (OTH) AF: 0.0886 AC: 187 AN: 2110

Alfa AF: 0.135 Hom.: 6499

Bravo AF: 0.120

Asia WGS AF: 0.149 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.83
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs2074488; hg19: chr6-31240431;