rs12741948

Variant names:

• chr1-65709181-C-T
• rs12741948
• ENST00000646875.2:n.348-1632C>T

Variant summary

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

The ENST00000646875.2(ENSG00000285079):​n.348-1632C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,030 control chromosomes in the GnomAD database, including 5,556 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 0.26 (5556 hom., cov: 31)
• Consequence: ENSG00000285079 ENST00000646875.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 2 publications found

Genes affected

ENSG00000285079 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.309 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
ENSG00000285079	ENST00000646875.2	n.348-1632C>T		intron_variant	Intron 1 of 2
ENSG00000285079	ENST00000760543.1	n.364+4875C>T		intron_variant	Intron 1 of 1
ENSG00000285079	ENST00000760544.1	n.291-1632C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39655 AN: 151912 Hom.: 5556 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0237

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.261 AC: 39670 AN: 152030 Hom.: 5556 Cov.: 31 AF XY: 0.257 AC XY: 19099 AN XY: 74332

African (AFR) AF: 0.205 AC: 8488 AN: 41472

American (AMR) AF: 0.276 AC: 4209 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3466

East Asian (EAS) AF: 0.0238 AC: 123 AN: 5176

South Asian (SAS) AF: 0.233 AC: 1122 AN: 4814

European-Finnish (FIN) AF: 0.247 AC: 2613 AN: 10564

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21220 AN: 67950

Other (OTH) AF: 0.269 AC: 568 AN: 2114

Alfa AF: 0.297 Hom.: 3227

Bravo AF: 0.261

Asia WGS AF: 0.110 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.69
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs12741948; hg19: chr1-66174864;