rs55694368

Variant names:

• chr2-238409051-G-T
• rs55694368

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 0.0723 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0185 AC: 770 AN: 41578

American (AMR) AF: 0.0614 AC: 940 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0650 AC: 225 AN: 3464

East Asian (EAS) AF: 0.0433 AC: 224 AN: 5170

South Asian (SAS) AF: 0.0452 AC: 218 AN: 4822

European-Finnish (FIN) AF: 0.111 AC: 1173 AN: 10600

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7242 AN: 68002

Other (OTH) AF: 0.0710 AC: 150 AN: 2112

Alfa AF: 0.0912 Hom.: 226

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
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs55694368; hg19: chr2-239317692;