6-32434687-T-C

Variant names:

• chr6-32434687-T-C
• rs7773756
• ENST00000766007.1:n.279+3457A>G

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.279+3457A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,012 control chromosomes in the GnomAD database, including 11,698 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 0.39 (11698 hom., cov: 31)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 26 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299747	ENST00000766007.1	n.279+3457A>G		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766247.1	n.*156T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58747 AN: 151894 Hom.: 11697 Cov.: 31

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.387 AC: 58768 AN: 152012 Hom.: 11698 Cov.: 31 AF XY: 0.389 AC XY: 28889 AN XY: 74300

African (AFR) AF: 0.342 AC: 14159 AN: 41454

American (AMR) AF: 0.447 AC: 6831 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1796 AN: 3470

East Asian (EAS) AF: 0.552 AC: 2850 AN: 5162

South Asian (SAS) AF: 0.521 AC: 2513 AN: 4820

European-Finnish (FIN) AF: 0.291 AC: 3075 AN: 10572

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26175 AN: 67946

Other (OTH) AF: 0.413 AC: 870 AN: 2108

Alfa AF: 0.393 Hom.: 28838

Bravo AF: 0.395

Asia WGS AF: 0.473 AC: 1643 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	5.9
DANN	Benign	0.71
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7773756; hg19: chr6-32402464;