rs3806792

Variant names:

• chr4-74099557-T-C
• rs3806792
• ENST00000688466.1:n.155T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000688466.1(ENSG00000289241):​n.155T>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 ENST00000688466.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.871

Genes affected

ENSG00000289241 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	ENST00000688466.1	n.155T>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

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.519

Alfa AF: 0.584 Hom.: 12127

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3806792; hg19: chr4-74965274;