rs3806792

Positions:

• chr4-74099557-T-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: ENST00000688466.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.871

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000688466.1	n.155T>C		non_coding_transcript_exon_variant	1/1

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;