rs3806792

Variant names:

• chr4-74099557-T-C
• rs3806792
• ENST00000688466.2:n.532T>C

Variant summary

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

The ENST00000688466.2(ENSG00000289241):​n.532T>C 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 0.498 in 152,080 control chromosomes in the GnomAD database, including 21,295 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 0.50 (21295 hom., cov: 32)
• Consequence: ENSG00000289241 ENST00000688466.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.871
• Publications: 17 publications found

Genes affected

ENSG00000289241 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.616 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
ENSG00000289241	ENST00000688466.2	n.532T>C		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75665 AN: 151962 Hom.: 21295 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.498 AC: 75673 AN: 152080 Hom.: 21295 Cov.: 32 AF XY: 0.502 AC XY: 37351 AN XY: 74336

African (AFR) AF: 0.222 AC: 9218 AN: 41500

American (AMR) AF: 0.626 AC: 9571 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2023 AN: 3468

East Asian (EAS) AF: 0.339 AC: 1745 AN: 5146

South Asian (SAS) AF: 0.549 AC: 2642 AN: 4816

European-Finnish (FIN) AF: 0.663 AC: 7019 AN: 10584

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41595 AN: 67968

Other (OTH) AF: 0.519 AC: 1096 AN: 2110

Alfa AF: 0.581 Hom.: 13549

Bravo AF: 0.484

Asia WGS AF: 0.409 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.7
DANN	Benign	0.60
PhyloP100		0.87
PromoterAI		-0.019	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3806792; hg19: chr4-74965274;