rs12407665

Variant names:

• chr1-13871220-T-C
• rs12407665
• ENST00000801165.1:n.232-1323T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-13871220-T-C
• chr1-13871220-T-G

Variant summary

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

The ENST00000801165.1(ENSG00000304226):​n.232-1323T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,084 control chromosomes in the GnomAD database, including 10,294 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 0.35 (10294 hom., cov: 32)
• Consequence: ENSG00000304226 ENST00000801165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 2 publications found

Genes affected

ENSG00000304226 (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 (EAS) allele frequency at 95% confidence interval = 0.703 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
ENSG00000304226	ENST00000801165.1	n.232-1323T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53059 AN: 151964 Hom.: 10274 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.349 AC: 53123 AN: 152084 Hom.: 10294 Cov.: 32 AF XY: 0.359 AC XY: 26703 AN XY: 74326

African (AFR) AF: 0.235 AC: 9762 AN: 41496

American (AMR) AF: 0.479 AC: 7325 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 969 AN: 3466

East Asian (EAS) AF: 0.722 AC: 3730 AN: 5166

South Asian (SAS) AF: 0.441 AC: 2123 AN: 4812

European-Finnish (FIN) AF: 0.451 AC: 4767 AN: 10578

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23287 AN: 67964

Other (OTH) AF: 0.358 AC: 756 AN: 2110

Alfa AF: 0.346 Hom.: 15722

Bravo AF: 0.350

Asia WGS AF: 0.570 AC: 1976 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	3.6
DANN	Benign	0.72
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs12407665; hg19: chr1-14197715;