rs1905178

Positions:

• chr3-65065992-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;