rs9258260

Positions:

• chr6-29755384-C-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, non coding transcript 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: ENST00000648999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648999.1	n.355+2457C>T		intron_variant, non_coding_transcript_variant

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;