3-103271406-C-T

Variant names:

• chr3-103271406-C-T
• rs1304118

Variant summary

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

The variant allele was found at a frequency of 0.104 in 152,152 control chromosomes in the GnomAD database, including 950 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 0.10 (950 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.164 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: 0.104 AC: 15841 AN: 152032 Hom.: 949 Cov.: 32

Gnomad AFR AF: 0.0711

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0261

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.104 AC: 15850 AN: 152152 Hom.: 950 Cov.: 32 AF XY: 0.103 AC XY: 7676 AN XY: 74392

African (AFR) AF: 0.0712 AC: 2956 AN: 41524

American (AMR) AF: 0.117 AC: 1784 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 464 AN: 3470

East Asian (EAS) AF: 0.0257 AC: 133 AN: 5172

South Asian (SAS) AF: 0.174 AC: 837 AN: 4818

European-Finnish (FIN) AF: 0.114 AC: 1211 AN: 10586

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 7991 AN: 67980

Other (OTH) AF: 0.116 AC: 244 AN: 2110

Alfa AF: 0.102 Hom.: 176

Bravo AF: 0.105

Asia WGS AF: 0.113 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.15
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1304118; hg19: chr3-102990250;