chr6-32432413-T-C

Variant names:

• chr6-32432413-T-C
• rs7762370
• ENST00000766007.1:n.280-1682A>G

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.280-1682A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0707 in 152,258 control chromosomes in the GnomAD database, including 546 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 0.071 (546 hom., cov: 32)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 8 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 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

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
	ENSG00000299747	ENST00000766007.1		n.280-1682A>G		intron	N/A
	ENSG00000299769	ENST00000766247.1		n.283-1679T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0707 AC: 10752 AN: 152140 Hom.: 546 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.0371

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.00828

Gnomad SAS AF: 0.0600

Gnomad FIN AF: 0.0163

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0512

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0707 AC: 10767 AN: 152258 Hom.: 546 Cov.: 32 AF XY: 0.0681 AC XY: 5072 AN XY: 74450

African (AFR) AF: 0.140 AC: 5820 AN: 41538

American (AMR) AF: 0.0371 AC: 567 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 74 AN: 3468

East Asian (EAS) AF: 0.00829 AC: 43 AN: 5184

South Asian (SAS) AF: 0.0594 AC: 287 AN: 4832

European-Finnish (FIN) AF: 0.0163 AC: 173 AN: 10616

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0512 AC: 3485 AN: 68012

Other (OTH) AF: 0.0649 AC: 137 AN: 2112

Alfa AF: 0.0581 Hom.: 499

Bravo AF: 0.0759

Asia WGS AF: 0.0280 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.7
DANN	Benign	0.85
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs7762370; hg19: chr6-32400190;