2-5113465-C-T

Variant names:

• chr2-5113465-C-T
• rs1075309

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 0.204 in 152,094 control chromosomes in the GnomAD database, including 3,980 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 (3980 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 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: 0.205 AC: 31106 AN: 151976 Hom.: 3986 Cov.: 33

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.204 AC: 31095 AN: 152094 Hom.: 3980 Cov.: 33 AF XY: 0.206 AC XY: 15352 AN XY: 74346

African (AFR) AF: 0.0736 AC: 3056 AN: 41538

American (AMR) AF: 0.194 AC: 2962 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 989 AN: 3468

East Asian (EAS) AF: 0.0128 AC: 66 AN: 5168

South Asian (SAS) AF: 0.238 AC: 1146 AN: 4816

European-Finnish (FIN) AF: 0.331 AC: 3484 AN: 10540

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18680 AN: 67980

Other (OTH) AF: 0.201 AC: 425 AN: 2112

Alfa AF: 0.221 Hom.: 753

Bravo AF: 0.184

Asia WGS AF: 0.132 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.9
DANN	Benign	0.59
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1075309; hg19: chr2-5253598;