rs12675001

Variant names:

• chr8-114107210-G-T
• rs12675001
• ENST00000759927.1:n.45+6430C>A

Variant summary

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

The ENST00000759927.1(ENSG00000299025):​n.45+6430C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 149,700 control chromosomes in the GnomAD database, including 8,753 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 0.34 (8753 hom., cov: 29)
• Consequence: ENSG00000299025 ENST00000759927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 2 publications found

Genes affected

ENSG00000299025 (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 (NFE) allele frequency at 95% confidence interval = 0.383 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
ENSG00000299025	ENST00000759927.1	n.45+6430C>A		intron_variant	Intron 1 of 2
ENSG00000299025	ENST00000759928.1	n.139+5664C>A		intron_variant	Intron 1 of 1
ENSG00000299025	ENST00000759929.1	n.139+5664C>A		intron_variant	Intron 1 of 2
ENSG00000299025	ENST00000759930.1	n.33+6430C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50345 AN: 149620 Hom.: 8753 Cov.: 29

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.336 AC: 50362 AN: 149700 Hom.: 8753 Cov.: 29 AF XY: 0.332 AC XY: 24235 AN XY: 72906

African (AFR) AF: 0.260 AC: 10610 AN: 40748

American (AMR) AF: 0.356 AC: 5307 AN: 14910

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1137 AN: 3458

East Asian (EAS) AF: 0.170 AC: 863 AN: 5076

South Asian (SAS) AF: 0.367 AC: 1738 AN: 4740

European-Finnish (FIN) AF: 0.325 AC: 3189 AN: 9810

Middle Eastern (MID) AF: 0.337 AC: 97 AN: 288

European-Non Finnish (NFE) AF: 0.387 AC: 26221 AN: 67686

Other (OTH) AF: 0.359 AC: 750 AN: 2088

Alfa AF: 0.367 Hom.: 26232

Bravo AF: 0.331

Asia WGS AF: 0.304 AC: 1058 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	0.81
DANN	Benign	0.50
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs12675001; hg19: chr8-115119439;