6-32477914-C-T

Variant names:

• chr6-32477914-C-T
• rs9378212
• ENST00000829864.1:n.273+3705C>T

Variant summary

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

The ENST00000829864.1(ENSG00000307923):​n.273+3705C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 149,372 control chromosomes in the GnomAD database, including 11,693 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 0.38 (11693 hom., cov: 36)
• Consequence: ENSG00000307923 ENST00000829864.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 21 publications found

Genes affected

ENSG00000307923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.423 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
ENSG00000307923	ENST00000829864.1	n.273+3705C>T		intron_variant	Intron 2 of 2
ENSG00000307923	ENST00000829865.1	n.270-1222C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.384 AC: 57333 AN: 149256 Hom.: 11686 Cov.: 36

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.384 AC: 57371 AN: 149372 Hom.: 11693 Cov.: 36 AF XY: 0.384 AC XY: 28042 AN XY: 73048

African (AFR) AF: 0.277 AC: 11201 AN: 40384

American (AMR) AF: 0.432 AC: 6514 AN: 15072

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1633 AN: 3440

East Asian (EAS) AF: 0.384 AC: 1938 AN: 5046

South Asian (SAS) AF: 0.346 AC: 1633 AN: 4714

European-Finnish (FIN) AF: 0.447 AC: 4637 AN: 10384

Middle Eastern (MID) AF: 0.314 AC: 91 AN: 290

European-Non Finnish (NFE) AF: 0.423 AC: 28343 AN: 67074

Other (OTH) AF: 0.389 AC: 803 AN: 2064

Alfa AF: 0.382 Hom.: 5238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.19
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9378212; hg19: chr6-32445691;