1-118660677-C-T

Variant names:

• chr1-118660677-C-T
• rs12143914
• ENST00000845043.1:n.321+12396C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000845043.1(ENSG00000309892):​n.321+12396C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0991 in 152,086 control chromosomes in the GnomAD database, including 941 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 0.099 (941 hom., cov: 32)
• Consequence: ENSG00000309892 ENST00000845043.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.38
• Publications: 6 publications found

Genes affected

ENSG00000309892 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 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
ENSG00000309892	ENST00000845043.1	n.321+12396C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0991 AC: 15060 AN: 151968 Hom.: 941 Cov.: 32

Gnomad AFR AF: 0.0449

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0964

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0771

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0710

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.0991 AC: 15067 AN: 152086 Hom.: 941 Cov.: 32 AF XY: 0.0981 AC XY: 7292 AN XY: 74338

African (AFR) AF: 0.0448 AC: 1862 AN: 41518

American (AMR) AF: 0.0962 AC: 1468 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 783 AN: 3468

East Asian (EAS) AF: 0.0769 AC: 396 AN: 5152

South Asian (SAS) AF: 0.160 AC: 769 AN: 4810

European-Finnish (FIN) AF: 0.0710 AC: 753 AN: 10608

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8619 AN: 67960

Other (OTH) AF: 0.131 AC: 277 AN: 2108

Alfa AF: 0.0626 Hom.: 84

Bravo AF: 0.0979

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	20
DANN	Benign	0.50
PhyloP100		3.4

Splicing

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

Other links and lift over

dbSNP: rs12143914; hg19: chr1-119203300;