6-32431410-C-A

Variant names:

• chr6-32431410-C-A
• rs4321864
• ENST00000766007.1:n.280-679G>T

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.280-679G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,828 control chromosomes in the GnomAD database, including 7,496 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 0.31 (7496 hom., cov: 31)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558
• Publications: 24 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 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.280-679G>T		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766247.1	n.283-2682C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46681 AN: 151710 Hom.: 7505 Cov.: 31

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.307 AC: 46683 AN: 151828 Hom.: 7496 Cov.: 31 AF XY: 0.308 AC XY: 22870 AN XY: 74204

African (AFR) AF: 0.241 AC: 9979 AN: 41430

American (AMR) AF: 0.350 AC: 5336 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1653 AN: 3460

East Asian (EAS) AF: 0.413 AC: 2130 AN: 5162

South Asian (SAS) AF: 0.319 AC: 1534 AN: 4812

European-Finnish (FIN) AF: 0.269 AC: 2837 AN: 10546

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.326 AC: 22147 AN: 67854

Other (OTH) AF: 0.305 AC: 643 AN: 2110

Alfa AF: 0.320 Hom.: 15816

Bravo AF: 0.313

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.44
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs4321864; hg19: chr6-32399187;