chr6-31379045-T-C

Variant names:

• chr6-31379045-T-C
• rs9266629
• ENST00000755446.1:n.327-2935T>C

Variant summary

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

The ENST00000755446.1(ENSG00000298426):​n.327-2935T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,164 control chromosomes in the GnomAD database, including 2,166 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 0.15 (2166 hom., cov: 34)
• Consequence: ENSG00000298426 ENST00000755446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 34 publications found

Genes affected

ENSG00000298426 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755446.1. 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
	ENSG00000298426	ENST00000755446.1		n.327-2935T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23220 AN: 152046 Hom.: 2165 Cov.: 34

Gnomad AFR AF: 0.0667

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0808

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.0770

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.153 AC: 23233 AN: 152164 Hom.: 2166 Cov.: 34 AF XY: 0.150 AC XY: 11131 AN XY: 74384

African (AFR) AF: 0.0666 AC: 2769 AN: 41550

American (AMR) AF: 0.103 AC: 1574 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0808 AC: 280 AN: 3466

East Asian (EAS) AF: 0.215 AC: 1112 AN: 5174

South Asian (SAS) AF: 0.0768 AC: 370 AN: 4816

European-Finnish (FIN) AF: 0.200 AC: 2121 AN: 10580

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14507 AN: 67960

Other (OTH) AF: 0.130 AC: 274 AN: 2112

Alfa AF: 0.177 Hom.: 6518

Bravo AF: 0.141

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.4
DANN	Benign	0.72
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs9266629; hg19: chr6-31346822;