rs1905178

Variant names:

• chr3-65065992-T-C
• rs1905178

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 0.128 in 152,250 control chromosomes in the GnomAD database, including 1,328 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 0.13 (1328 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 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: 0.128 AC: 19497 AN: 152132 Hom.: 1323 Cov.: 33

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0802

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.128 AC: 19525 AN: 152250 Hom.: 1328 Cov.: 33 AF XY: 0.127 AC XY: 9442 AN XY: 74428

African (AFR) AF: 0.169 AC: 7003 AN: 41538

American (AMR) AF: 0.0805 AC: 1230 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3472

East Asian (EAS) AF: 0.101 AC: 523 AN: 5178

South Asian (SAS) AF: 0.154 AC: 740 AN: 4818

European-Finnish (FIN) AF: 0.106 AC: 1128 AN: 10608

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7963 AN: 68026

Other (OTH) AF: 0.118 AC: 249 AN: 2116

Alfa AF: 0.129 Hom.: 217

Bravo AF: 0.126

Asia WGS AF: 0.101 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.6
DANN	Benign	0.75
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs1905178; hg19: chr3-65051667;