chr6-29755384-C-T

Variant names:

• chr6-29755384-C-T
• rs9258260
• ENST00000648999.1:n.355+2457C>T

Variant summary

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

The ENST00000648999.1(ENSG00000285761):​n.355+2457C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,222 control chromosomes in the GnomAD database, including 1,240 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 0.12 (1240 hom., cov: 33)
• Consequence: ENSG00000285761 ENST00000648999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806

Genes affected

ENSG00000285761 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 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
ENSG00000285761	ENST00000648999.1	n.355+2457C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17705 AN: 152104 Hom.: 1236 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0914

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0937

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.116 AC: 17722 AN: 152222 Hom.: 1240 Cov.: 33 AF XY: 0.117 AC XY: 8743 AN XY: 74442

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0912

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.0600

Gnomad4 NFE AF: 0.0937

Gnomad4 OTH AF: 0.120

Alfa AF: 0.103 Hom.: 1319

Bravo AF: 0.119

Asia WGS AF: 0.208 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.95
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9258260; hg19: chr6-29723161;