2-5117223-T-C

Variant names:

• chr2-5117223-T-C
• rs1869410

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 0.205 in 152,010 control chromosomes in the GnomAD database, including 3,998 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 (3998 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551
• 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 = 0.272 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: 31173 AN: 151892 Hom.: 4004 Cov.: 32

Gnomad AFR AF: 0.0742

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0130

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.205 AC: 31161 AN: 152010 Hom.: 3998 Cov.: 32 AF XY: 0.207 AC XY: 15393 AN XY: 74284

African (AFR) AF: 0.0741 AC: 3073 AN: 41484

American (AMR) AF: 0.194 AC: 2970 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 990 AN: 3466

East Asian (EAS) AF: 0.0128 AC: 66 AN: 5158

South Asian (SAS) AF: 0.238 AC: 1146 AN: 4820

European-Finnish (FIN) AF: 0.331 AC: 3485 AN: 10538

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

European-Non Finnish (NFE) AF: 0.275 AC: 18713 AN: 67946

Other (OTH) AF: 0.204 AC: 431 AN: 2114

Alfa AF: 0.248 Hom.: 21429

Bravo AF: 0.184

Asia WGS AF: 0.133 AC: 466 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	1.1
DANN	Benign	0.66
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1869410; hg19: chr2-5257356;