rs55694368

Variant names:

• chr2-238409051-G-T
• rs55694368

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 0.0723 in 152,252 control chromosomes in the GnomAD database, including 543 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 0.072 (543 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 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: 0.0723 AC: 11000 AN: 152134 Hom.: 543 Cov.: 32

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.0615

Gnomad ASJ AF: 0.0650

Gnomad EAS AF: 0.0434

Gnomad SAS AF: 0.0450

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0723 AC: 11001 AN: 152252 Hom.: 543 Cov.: 32 AF XY: 0.0704 AC XY: 5239 AN XY: 74456

Gnomad4 AFR AF: 0.0185

Gnomad4 AMR AF: 0.0614

Gnomad4 ASJ AF: 0.0650

Gnomad4 EAS AF: 0.0433

Gnomad4 SAS AF: 0.0452

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0710

Alfa AF: 0.0910 Hom.: 126

Bravo AF: 0.0674

Asia WGS AF: 0.0470 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55694368; hg19: chr2-239317692;