6-32445317-A-G

Variant names:

• chr6-32445317-A-G
• rs2213586
• ENST00000766007.1:n.163-7057T>C

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.163-7057T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,702 control chromosomes in the GnomAD database, including 29,065 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 0.62 (29065 hom., cov: 30)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 38 publications found

Genes affected

ENSG00000299747 (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 (SAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766007.1. 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
	ENSG00000299747	ENST00000766007.1		n.163-7057T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93290 AN: 151582 Hom.: 29045 Cov.: 30

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.615 AC: 93354 AN: 151702 Hom.: 29065 Cov.: 30 AF XY: 0.616 AC XY: 45694 AN XY: 74132

African (AFR) AF: 0.597 AC: 24668 AN: 41346

American (AMR) AF: 0.669 AC: 10175 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2591 AN: 3470

East Asian (EAS) AF: 0.705 AC: 3630 AN: 5152

South Asian (SAS) AF: 0.742 AC: 3543 AN: 4776

European-Finnish (FIN) AF: 0.515 AC: 5414 AN: 10518

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41040 AN: 67928

Other (OTH) AF: 0.651 AC: 1369 AN: 2104

Alfa AF: 0.606 Hom.: 81258

Asia WGS AF: 0.669 AC: 2329 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	3.2
DANN	Benign	0.56
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs2213586; hg19: chr6-32413094;