rs1373494

Variant names:

• chr4-33746904-A-C
• rs1373494

Your query was ambiguous. Multiple possible variants found:

• chr4-33746904-A-C
• chr4-33746904-A-G
• chr4-33746904-A-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 0.203 in 152,138 control chromosomes in the GnomAD database, including 4,555 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 0.20 (4555 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 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: 0.202 AC: 30771 AN: 152020 Hom.: 4543 Cov.: 33

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0953

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.203 AC: 30815 AN: 152138 Hom.: 4555 Cov.: 33 AF XY: 0.205 AC XY: 15277 AN XY: 74368

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0954

Gnomad4 OTH AF: 0.181

Alfa AF: 0.181 Hom.: 682

Bravo AF: 0.216

Asia WGS AF: 0.289 AC: 1005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1373494; hg19: chr4-33748526;