3-164137281-C-T

Variant names:

• chr3-164137281-C-T
• rs78661745
• XR_001740997.2:n.1103+56227G>A

Variant summary

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

The XR_001740997.2(LOC102724419):​n.1103+56227G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0891 in 152,064 control chromosomes in the GnomAD database, including 738 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 0.089 (738 hom., cov: 32)
• Consequence: LOC102724419 XR_001740997.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631
• Publications: 3 publications found

Genes affected

LOC102724419 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.194 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: 0.0892 AC: 13548 AN: 151946 Hom.: 740 Cov.: 32

Gnomad AFR AF: 0.0293

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0977

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

GnomAD4 genome AF: 0.0891 AC: 13548 AN: 152064 Hom.: 738 Cov.: 32 AF XY: 0.0904 AC XY: 6717 AN XY: 74308

African (AFR) AF: 0.0292 AC: 1213 AN: 41512

American (AMR) AF: 0.124 AC: 1887 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0778 AC: 270 AN: 3470

East Asian (EAS) AF: 0.112 AC: 581 AN: 5174

South Asian (SAS) AF: 0.204 AC: 985 AN: 4820

European-Finnish (FIN) AF: 0.103 AC: 1086 AN: 10570

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7256 AN: 67958

Other (OTH) AF: 0.0981 AC: 207 AN: 2110

Alfa AF: 0.0911 Hom.: 479

Bravo AF: 0.0867

Asia WGS AF: 0.133 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.62
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs78661745; hg19: chr3-163855069;