rs751194

Positions:

• chr3-55453400-G-A
• chr3-55453400-G-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 0.434 in 151,924 control chromosomes in the GnomAD database, including 14,804 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 0.43 (14804 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 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: 0.434 AC: 65912 AN: 151806 Hom.: 14800 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.434 AC: 65934 AN: 151924 Hom.: 14804 Cov.: 32 AF XY: 0.434 AC XY: 32269 AN XY: 74280

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.455

Alfa AF: 0.459 Hom.: 33616

Bravo AF: 0.446

Asia WGS AF: 0.470 AC: 1631 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.017
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs751194; hg19: chr3-55487428;