rs12741825

Variant names:

• chr1-159700355-C-T
• rs12741825
• ENST00000751816.1:n.108-26172C>T

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-26172C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,152 control chromosomes in the GnomAD database, including 5,296 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 0.24 (5296 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 6 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 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
ENSG00000297913	ENST00000751816.1	n.108-26172C>T		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-26172C>T		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-26172C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36051 AN: 152034 Hom.: 5295 Cov.: 32

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0610

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.237 AC: 36068 AN: 152152 Hom.: 5296 Cov.: 32 AF XY: 0.240 AC XY: 17818 AN XY: 74384

African (AFR) AF: 0.0715 AC: 2972 AN: 41550

American (AMR) AF: 0.303 AC: 4640 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3472

East Asian (EAS) AF: 0.0609 AC: 315 AN: 5170

South Asian (SAS) AF: 0.244 AC: 1176 AN: 4824

European-Finnish (FIN) AF: 0.348 AC: 3682 AN: 10568

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.314 AC: 21305 AN: 67958

Other (OTH) AF: 0.254 AC: 535 AN: 2110

Alfa AF: 0.248 Hom.: 836

Bravo AF: 0.229

Asia WGS AF: 0.161 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.60
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs12741825; hg19: chr1-159670145;