rs3795743

Variant names:

• chr1-223108808-A-G
• rs3795743
• ENST00000762836.1:n.20A>G

Variant summary

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

The ENST00000762836.1(ENSG00000299361):​n.20A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,106 control chromosomes in the GnomAD database, including 9,982 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 (9982 hom., cov: 32)
• Consequence: ENSG00000299361 ENST00000762836.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762836.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299361	ENST00000762836.1		n.20A>G		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000299361	ENST00000762837.1		n.20A>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000299361	ENST00000762835.1		n.-82A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51275 AN: 151988 Hom.: 9978 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.337 AC: 51306 AN: 152106 Hom.: 9982 Cov.: 32 AF XY: 0.340 AC XY: 25272 AN XY: 74338

African (AFR) AF: 0.145 AC: 6002 AN: 41522

American (AMR) AF: 0.324 AC: 4950 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1407 AN: 3472

East Asian (EAS) AF: 0.209 AC: 1082 AN: 5172

South Asian (SAS) AF: 0.425 AC: 2042 AN: 4808

European-Finnish (FIN) AF: 0.493 AC: 5211 AN: 10566

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

European-Non Finnish (NFE) AF: 0.432 AC: 29331 AN: 67966

Other (OTH) AF: 0.338 AC: 714 AN: 2112

Alfa AF: 0.395 Hom.: 15598

Bravo AF: 0.312

Asia WGS AF: 0.302 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.040
DANN	Benign	0.21
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs3795743; hg19: chr1-223282150;