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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.399 AC: 16562 AN: 41482

American (AMR) AF: 0.211 AC: 3222 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3472

East Asian (EAS) AF: 0.319 AC: 1649 AN: 5170

South Asian (SAS) AF: 0.156 AC: 753 AN: 4814

European-Finnish (FIN) AF: 0.115 AC: 1214 AN: 10594

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0954 AC: 6484 AN: 68002

Other (OTH) AF: 0.181 AC: 381 AN: 2110

Alfa AF: 0.188 Hom.: 753

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
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs1373494; hg19: chr4-33748526;