rs751194

Variant names:

• chr3-55453400-G-A
• rs751194

Your query was ambiguous. Multiple possible variants found:

• chr3-55453400-G-A
• chr3-55453400-G-C

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 0.434 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.342 AC: 14149 AN: 41406

American (AMR) AF: 0.567 AC: 8663 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1522 AN: 3470

East Asian (EAS) AF: 0.597 AC: 3080 AN: 5156

South Asian (SAS) AF: 0.408 AC: 1963 AN: 4814

European-Finnish (FIN) AF: 0.389 AC: 4101 AN: 10538

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30852 AN: 67954

Other (OTH) AF: 0.455 AC: 958 AN: 2104

Alfa AF: 0.454 Hom.: 51627

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs751194; hg19: chr3-55487428;