rs3934834

Variant names:

• chr1-1070426-C-T
• rs3934834
• ENST00000800220.1:n.97+286C>T

Variant summary

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

The ENST00000800220.1(ENSG00000304169):​n.97+286C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,176 control chromosomes in the GnomAD database, including 3,668 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 0.20 (3668 hom., cov: 34)
• Consequence: ENSG00000304169 ENST00000800220.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 32 publications found

Genes affected

ENSG00000304169 (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 = 0.311 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
ENSG00000304169	ENST00000800220.1	n.97+286C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31065 AN: 152058 Hom.: 3663 Cov.: 34

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.204 AC: 31098 AN: 152176 Hom.: 3668 Cov.: 34 AF XY: 0.207 AC XY: 15424 AN XY: 74388

African (AFR) AF: 0.315 AC: 13100 AN: 41524

American (AMR) AF: 0.130 AC: 1995 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3470

East Asian (EAS) AF: 0.116 AC: 603 AN: 5178

South Asian (SAS) AF: 0.212 AC: 1024 AN: 4824

European-Finnish (FIN) AF: 0.243 AC: 2574 AN: 10594

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10512 AN: 67966

Other (OTH) AF: 0.185 AC: 392 AN: 2114

Alfa AF: 0.166 Hom.: 3942

Bravo AF: 0.198

Asia WGS AF: 0.165 AC: 571 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	8.4
DANN	Benign	0.54
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3934834; hg19: chr1-1005806;