1-109643941-C-T

Variant names:

• chr1-109643941-C-T
• rs12745189
• ENST00000839259.1:n.295-26C>T

Variant summary

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

The ENST00000839259.1(ENSG00000309177):​n.295-26C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,712 control chromosomes in the GnomAD database, including 17,797 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 0.48 (17797 hom., cov: 30)
• Consequence: ENSG00000309177 ENST00000839259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.96
• Publications: 27 publications found

Genes affected

ENSG00000309177 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 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
ENSG00000309177	ENST00000839259.1	n.295-26C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72770 AN: 151594 Hom.: 17777 Cov.: 30

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.480 AC: 72841 AN: 151712 Hom.: 17797 Cov.: 30 AF XY: 0.486 AC XY: 36070 AN XY: 74148

African (AFR) AF: 0.457 AC: 18877 AN: 41344

American (AMR) AF: 0.582 AC: 8884 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1681 AN: 3466

East Asian (EAS) AF: 0.663 AC: 3376 AN: 5090

South Asian (SAS) AF: 0.421 AC: 2024 AN: 4804

European-Finnish (FIN) AF: 0.546 AC: 5755 AN: 10546

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.454 AC: 30804 AN: 67888

Other (OTH) AF: 0.501 AC: 1056 AN: 2106

Alfa AF: 0.461 Hom.: 26545

Bravo AF: 0.486

Asia WGS AF: 0.543 AC: 1887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	11
DANN	Benign	0.75
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs12745189; hg19: chr1-110186563;