rs3847228

Variant names:

• chr9-1798805-C-T
• rs3847228
• XR_001746599.1:n.142+79893C>T

Variant summary

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

The XR_001746599.1(LOC105375951):​n.142+79893C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 151,826 control chromosomes in the GnomAD database, including 8,091 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 0.29 (8091 hom., cov: 31)
• Consequence: LOC105375951 XR_001746599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922
• Publications: 4 publications found

Genes affected

LOC105375951 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44195 AN: 151706 Hom.: 8089 Cov.: 31

Gnomad AFR AF: 0.0815

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.359

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.291 AC: 44190 AN: 151826 Hom.: 8091 Cov.: 31 AF XY: 0.289 AC XY: 21470 AN XY: 74166

African (AFR) AF: 0.0812 AC: 3366 AN: 41446

American (AMR) AF: 0.282 AC: 4297 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1005 AN: 5154

South Asian (SAS) AF: 0.258 AC: 1237 AN: 4796

European-Finnish (FIN) AF: 0.433 AC: 4552 AN: 10504

Middle Eastern (MID) AF: 0.366 AC: 106 AN: 290

European-Non Finnish (NFE) AF: 0.408 AC: 27677 AN: 67900

Other (OTH) AF: 0.279 AC: 589 AN: 2110

Alfa AF: 0.344 Hom.: 19869

Bravo AF: 0.266

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.29
DANN	Benign	0.63
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs3847228; hg19: chr9-1798805; COSMIC: COSV69442186;