6-14142258-G-C

Variant names:

• chr6-14142258-G-C
• rs853369
• ENST00000724695.1:n.501-741C>G

Variant summary

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

The ENST00000724695.1(ENSG00000285639):​n.501-741C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 150,588 control chromosomes in the GnomAD database, including 29,538 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 0.62 (29538 hom., cov: 25)
• Consequence: ENSG00000285639 ENST00000724695.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 3 publications found

Genes affected

ENSG00000285639 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 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
ENSG00000285639	ENST00000724695.1	n.501-741C>G		intron_variant	Intron 3 of 3
ENSG00000285639	ENST00000724696.1	n.495-741C>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93208 AN: 150468 Hom.: 29492 Cov.: 25

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.620 AC: 93323 AN: 150588 Hom.: 29538 Cov.: 25 AF XY: 0.617 AC XY: 45344 AN XY: 73482

African (AFR) AF: 0.682 AC: 27904 AN: 40892

American (AMR) AF: 0.636 AC: 9613 AN: 15112

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2231 AN: 3462

East Asian (EAS) AF: 0.176 AC: 894 AN: 5068

South Asian (SAS) AF: 0.491 AC: 2305 AN: 4694

European-Finnish (FIN) AF: 0.640 AC: 6660 AN: 10402

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41699 AN: 67684

Other (OTH) AF: 0.620 AC: 1289 AN: 2078

Alfa AF: 0.501 Hom.: 1369

Bravo AF: 0.623

Asia WGS AF: 0.358 AC: 1248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.43
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs853369; hg19: chr6-14142489;