rs3943367

Variant names:

• chr18-75815872-T-C
• rs3943367

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 0.0526 in 152,238 control chromosomes in the GnomAD database, including 504 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 0.053 (504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

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 = 0.149 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: 0.0525 AC: 7985 AN: 152120 Hom.: 504 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0273

Gnomad ASJ AF: 0.00692

Gnomad EAS AF: 0.0661

Gnomad SAS AF: 0.00725

Gnomad FIN AF: 0.0197

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00792

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0526 AC: 8003 AN: 152238 Hom.: 504 Cov.: 32 AF XY: 0.0521 AC XY: 3875 AN XY: 74434

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0275

Gnomad4 ASJ AF: 0.00692

Gnomad4 EAS AF: 0.0659

Gnomad4 SAS AF: 0.00725

Gnomad4 FIN AF: 0.0197

Gnomad4 NFE AF: 0.00792

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0194 Hom.: 130

Bravo AF: 0.0576

Asia WGS AF: 0.0510 AC: 179 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	1.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3943367; hg19: chr18-73527827;