rs3776083

chr5-150188407-G-Achr5-150188407-G-Cchr5-150188407-G-T

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 0.333 in 152,126 control chromosomes in the GnomAD database, including 9,145 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 0.33 (9145 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50714 AN: 152008 Hom.: 9147 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.333 AC: 50710 AN: 152126 Hom.: 9145 Cov.: 33 AF XY: 0.334 AC XY: 24822 AN XY: 74378

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.372

Alfa AF: 0.316 Hom.: 2624

Bravo AF: 0.323

Asia WGS AF: 0.372 AC: 1292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.21
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3776083; hg19: chr5-149567970;