rs3795742

Variant names:

• chr1-223108694-A-G
• rs3795742
• ENST00000762835.1:n.-196A>G

Variant summary

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

The ENST00000762835.1(ENSG00000299361):​n.-196A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,076 control chromosomes in the GnomAD database, including 10,113 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 0.34 (10113 hom., cov: 32)
• Consequence: ENSG00000299361 ENST00000762835.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 0 publications found

Genes affected

ENSG00000299361 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 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
ENSG00000299361	ENST00000762835.1	n.-196A>G		upstream_gene_variant
ENSG00000299361	ENST00000762836.1	n.-95A>G		upstream_gene_variant
ENSG00000299361	ENST00000762837.1	n.-95A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51577 AN: 151958 Hom.: 10110 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.339 AC: 51607 AN: 152076 Hom.: 10113 Cov.: 32 AF XY: 0.342 AC XY: 25443 AN XY: 74344

African (AFR) AF: 0.145 AC: 6023 AN: 41516

American (AMR) AF: 0.325 AC: 4959 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1395 AN: 3472

East Asian (EAS) AF: 0.209 AC: 1081 AN: 5164

South Asian (SAS) AF: 0.424 AC: 2043 AN: 4814

European-Finnish (FIN) AF: 0.500 AC: 5281 AN: 10560

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29539 AN: 67952

Other (OTH) AF: 0.340 AC: 719 AN: 2114

Alfa AF: 0.394 Hom.: 1588

Bravo AF: 0.314

Asia WGS AF: 0.303 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.79
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs3795742; hg19: chr1-223282036;