3-146185639-G-T

Variant names:

• chr3-146185639-G-T
• rs11928424
• XR_001740949.2:n.740+4160C>A

Variant summary

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

The XR_001740949.2(LOC105374145):​n.740+4160C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 151,966 control chromosomes in the GnomAD database, including 1,033 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 0.11 (1033 hom., cov: 32)
• Consequence: LOC105374145 XR_001740949.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• Publications: 0 publications found

Genes affected

LOC105374145 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.141 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: 0.115 AC: 17420 AN: 151850 Hom.: 1030 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0827

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0343

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.115 AC: 17440 AN: 151966 Hom.: 1033 Cov.: 32 AF XY: 0.114 AC XY: 8434 AN XY: 74290

African (AFR) AF: 0.116 AC: 4806 AN: 41452

American (AMR) AF: 0.0826 AC: 1259 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3470

East Asian (EAS) AF: 0.0346 AC: 179 AN: 5174

South Asian (SAS) AF: 0.150 AC: 720 AN: 4814

European-Finnish (FIN) AF: 0.110 AC: 1162 AN: 10554

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8398 AN: 67942

Other (OTH) AF: 0.118 AC: 249 AN: 2106

Alfa AF: 0.117 Hom.: 1858

Bravo AF: 0.112

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.50
DANN	Benign	0.12
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs11928424; hg19: chr3-145903426;