rs3842204

Variant names:

• chr8-6926777-AT-A
• rs3842204
• ENST00000734108.1:n.367-15delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000734108.1(ENSG00000295932):​n.367-15delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0718 in 152,218 control chromosomes in the GnomAD database, including 558 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.072 (558 hom., cov: 32)
• Consequence: ENSG00000295932 ENST00000734108.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 1 publications found

Genes affected

ENSG00000295932 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 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
ENSG00000295932	ENST00000734108.1	n.367-15delT		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0719 AC: 10929 AN: 152100 Hom.: 558 Cov.: 32

Gnomad AFR AF: 0.0286

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.0870

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0628

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0718 AC: 10936 AN: 152218 Hom.: 558 Cov.: 32 AF XY: 0.0784 AC XY: 5838 AN XY: 74422

African (AFR) AF: 0.0286 AC: 1190 AN: 41544

American (AMR) AF: 0.138 AC: 2113 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0873 AC: 303 AN: 3472

East Asian (EAS) AF: 0.228 AC: 1179 AN: 5178

South Asian (SAS) AF: 0.0869 AC: 419 AN: 4824

European-Finnish (FIN) AF: 0.116 AC: 1234 AN: 10594

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0628 AC: 4269 AN: 67990

Other (OTH) AF: 0.0634 AC: 134 AN: 2112

Alfa AF: 0.0719 Hom.: 57

Bravo AF: 0.0714

Asia WGS AF: 0.154 AC: 536 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3842204; hg19: chr8-6784299;