rs9859392

Variant names:

• chr3-41193025-C-G
• rs9859392
• ENST00000775825.1:n.428G>C

Your query was ambiguous. Multiple possible variants found:

• chr3-41193025-C-G
• chr3-41193025-C-T

Variant summary

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

The ENST00000775825.1(ENSG00000233919):​n.428G>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 0.392 in 151,978 control chromosomes in the GnomAD database, including 12,157 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 0.39 (12157 hom., cov: 32)
• Consequence: ENSG00000233919 ENST00000775825.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 13 publications found

Genes affected

ENSG00000233919 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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
ENSG00000233919	ENST00000775825.1	n.428G>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000233919	ENST00000775826.1	n.606G>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000233919	ENST00000775827.1	n.394G>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000233919	ENST00000775824.1	n.56+3459G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59550 AN: 151860 Hom.: 12152 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.392 AC: 59579 AN: 151978 Hom.: 12157 Cov.: 32 AF XY: 0.389 AC XY: 28892 AN XY: 74266

African (AFR) AF: 0.294 AC: 12184 AN: 41438

American (AMR) AF: 0.362 AC: 5531 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1423 AN: 3468

East Asian (EAS) AF: 0.249 AC: 1288 AN: 5176

South Asian (SAS) AF: 0.404 AC: 1943 AN: 4812

European-Finnish (FIN) AF: 0.459 AC: 4833 AN: 10524

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31058 AN: 67968

Other (OTH) AF: 0.385 AC: 814 AN: 2112

Alfa AF: 0.405 Hom.: 1596

Bravo AF: 0.381

Asia WGS AF: 0.360 AC: 1254 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.59
DANN	Benign	0.50
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs9859392; hg19: chr3-41234516;