chr6-141466657-T-C

Variant names:

• chr6-141466657-T-C
• rs4386830
• ENST00000763028.1:n.167-330A>G

Variant summary

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

The ENST00000763028.1(ENSG00000299379):​n.167-330A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,006 control chromosomes in the GnomAD database, including 7,821 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 0.32 (7821 hom., cov: 32)
• Consequence: ENSG00000299379 ENST00000763028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 3 publications found

Genes affected

ENSG00000299379 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 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
ENSG00000299379	ENST00000763028.1	n.167-330A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47988 AN: 151888 Hom.: 7811 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.316 AC: 48030 AN: 152006 Hom.: 7821 Cov.: 32 AF XY: 0.319 AC XY: 23715 AN XY: 74310

African (AFR) AF: 0.297 AC: 12310 AN: 41452

American (AMR) AF: 0.330 AC: 5038 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3472

East Asian (EAS) AF: 0.371 AC: 1903 AN: 5134

South Asian (SAS) AF: 0.387 AC: 1858 AN: 4806

European-Finnish (FIN) AF: 0.225 AC: 2383 AN: 10596

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21858 AN: 67956

Other (OTH) AF: 0.350 AC: 738 AN: 2110

Alfa AF: 0.325 Hom.: 10445

Bravo AF: 0.318

Asia WGS AF: 0.389 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.43
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4386830; hg19: chr6-141787794;