rs1905178

Variant names:

• chr3-65065992-T-C
• rs1905178

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0805

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.118

Alfa AF: 0.128 Hom.: 204

Bravo AF: 0.126

Asia WGS AF: 0.101 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1905178; hg19: chr3-65051667;