rs1742848

Variant names:

• chr1-118657073-C-T
• rs1742848
• ENST00000845043.1:n.321+8792C>T

Variant summary

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

The ENST00000845043.1(ENSG00000309892):​n.321+8792C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,520 control chromosomes in the GnomAD database, including 23,592 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 0.53 (23592 hom., cov: 31)
• Consequence: ENSG00000309892 ENST00000845043.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 5 publications found

Genes affected

ENSG00000309892 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.647 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+8792C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80568 AN: 151404 Hom.: 23589 Cov.: 31

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.698

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.532 AC: 80584 AN: 151520 Hom.: 23592 Cov.: 31 AF XY: 0.533 AC XY: 39481 AN XY: 74022

African (AFR) AF: 0.272 AC: 11243 AN: 41370

American (AMR) AF: 0.599 AC: 9107 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2207 AN: 3468

East Asian (EAS) AF: 0.424 AC: 2174 AN: 5126

South Asian (SAS) AF: 0.587 AC: 2819 AN: 4800

European-Finnish (FIN) AF: 0.651 AC: 6808 AN: 10462

Middle Eastern (MID) AF: 0.699 AC: 200 AN: 286

European-Non Finnish (NFE) AF: 0.652 AC: 44230 AN: 67802

Other (OTH) AF: 0.572 AC: 1203 AN: 2102

Alfa AF: 0.610 Hom.: 26643

Bravo AF: 0.516

Asia WGS AF: 0.503 AC: 1732 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.23
DANN	Benign	0.43
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1742848; hg19: chr1-119199696;