rs3754093

Variant names:

• chr1-241846814-A-G
• rs3754093
• ENST00000684005.2:n.168+1155T>C

Variant summary

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

The ENST00000684005.2(ENSG00000288723):​n.168+1155T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,116 control chromosomes in the GnomAD database, including 4,604 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 0.23 (4604 hom., cov: 32)
• Consequence: ENSG00000288723 ENST00000684005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419
• Publications: 14 publications found

Genes affected

ENSG00000288723 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.374 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
ENSG00000288723	ENST00000684005.2	n.168+1155T>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35169 AN: 151998 Hom.: 4589 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.0965

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.231 AC: 35208 AN: 152116 Hom.: 4604 Cov.: 32 AF XY: 0.233 AC XY: 17355 AN XY: 74362

African (AFR) AF: 0.285 AC: 11841 AN: 41482

American (AMR) AF: 0.320 AC: 4886 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3470

East Asian (EAS) AF: 0.388 AC: 2005 AN: 5168

South Asian (SAS) AF: 0.389 AC: 1869 AN: 4808

European-Finnish (FIN) AF: 0.0965 AC: 1022 AN: 10592

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

European-Non Finnish (NFE) AF: 0.175 AC: 11869 AN: 68002

Other (OTH) AF: 0.265 AC: 558 AN: 2106

Alfa AF: 0.210 Hom.: 5445

Bravo AF: 0.250

Asia WGS AF: 0.362 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.59
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs3754093; hg19: chr1-242010116;