chr6-31353550-A-G

Variant names:

• chr6-31353550-A-G
• rs9266095
• ENST00000755297.1:n.33-2651A>G

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.33-2651A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,100 control chromosomes in the GnomAD database, including 6,899 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 0.30 (6899 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 7 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755297.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298396	ENST00000755297.1		n.33-2651A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44834 AN: 151982 Hom.: 6881 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.295 AC: 44880 AN: 152100 Hom.: 6899 Cov.: 32 AF XY: 0.304 AC XY: 22589 AN XY: 74358

African (AFR) AF: 0.325 AC: 13495 AN: 41476

American (AMR) AF: 0.316 AC: 4840 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1078 AN: 3472

East Asian (EAS) AF: 0.472 AC: 2441 AN: 5170

South Asian (SAS) AF: 0.368 AC: 1773 AN: 4824

European-Finnish (FIN) AF: 0.364 AC: 3845 AN: 10564

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16425 AN: 67982

Other (OTH) AF: 0.313 AC: 661 AN: 2110

Alfa AF: 0.282 Hom.: 1536

Bravo AF: 0.291

Asia WGS AF: 0.342 AC: 1188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.3
DANN	Benign	0.54
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs9266095; hg19: chr6-31321327;