rs3821947

Variant names:

• chr4-4858411-A-G
• rs3821947
• ENST00000834197.1:n.37T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-4858411-A-G
• chr4-4858411-A-T

Variant summary

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

The ENST00000834197.1(ENSG00000308455):​n.37T>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 0.596 in 151,932 control chromosomes in the GnomAD database, including 28,300 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 0.60 (28300 hom., cov: 32)
• Consequence: ENSG00000308455 ENST00000834197.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.482
• Publications: 5 publications found

Genes affected

ENSG00000308455 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 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
ENSG00000308455	ENST00000834197.1	n.37T>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000308455	ENST00000834195.1	n.304-1622T>C		intron_variant	Intron 2 of 2
ENSG00000308455	ENST00000834196.1	n.49-1622T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90496 AN: 151814 Hom.: 28240 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.596 AC: 90613 AN: 151932 Hom.: 28300 Cov.: 32 AF XY: 0.604 AC XY: 44835 AN XY: 74258

African (AFR) AF: 0.778 AC: 32240 AN: 41454

American (AMR) AF: 0.627 AC: 9584 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2030 AN: 3468

East Asian (EAS) AF: 0.544 AC: 2809 AN: 5166

South Asian (SAS) AF: 0.592 AC: 2853 AN: 4822

European-Finnish (FIN) AF: 0.617 AC: 6492 AN: 10516

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32921 AN: 67896

Other (OTH) AF: 0.567 AC: 1196 AN: 2110

Alfa AF: 0.515 Hom.: 26729

Bravo AF: 0.603

Asia WGS AF: 0.558 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.8
DANN	Benign	0.53
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs3821947; hg19: chr4-4860138;