rs9295822

Positions:

• chr6-29861103-C-T

Variant summary

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

The ENST00000647952.1(ENSG00000290870):​n.2063-3665G>A 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 0.112 in 152,166 control chromosomes in the GnomAD database, including 1,424 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 0.11 (1424 hom., cov: 31)
• Consequence: ENST00000647952.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 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
	ENST00000647952.1	n.2063-3665G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16994 AN: 152048 Hom.: 1422 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.0245

Gnomad SAS AF: 0.0676

Gnomad FIN AF: 0.0525

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0535

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.112 AC: 17011 AN: 152166 Hom.: 1424 Cov.: 31 AF XY: 0.111 AC XY: 8280 AN XY: 74412

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0749

Gnomad4 EAS AF: 0.0245

Gnomad4 SAS AF: 0.0674

Gnomad4 FIN AF: 0.0525

Gnomad4 NFE AF: 0.0535

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0761 Hom.: 361

Bravo AF: 0.126

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9295822; hg19: chr6-29828880;