2-205679578-C-T

Variant names:

• chr2-205679578-C-T
• rs1517527

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 0.388 in 151,976 control chromosomes in the GnomAD database, including 12,525 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 0.39 (12525 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 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: 0.388 AC: 58936 AN: 151858 Hom.: 12524 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.388 AC: 58968 AN: 151976 Hom.: 12525 Cov.: 32 AF XY: 0.394 AC XY: 29245 AN XY: 74250

African (AFR) AF: 0.217 AC: 8985 AN: 41476

American (AMR) AF: 0.396 AC: 6052 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1497 AN: 3470

East Asian (EAS) AF: 0.583 AC: 3008 AN: 5162

South Asian (SAS) AF: 0.532 AC: 2562 AN: 4812

European-Finnish (FIN) AF: 0.521 AC: 5494 AN: 10536

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29982 AN: 67936

Other (OTH) AF: 0.386 AC: 816 AN: 2112

Alfa AF: 0.429 Hom.: 11409

Bravo AF: 0.371

Asia WGS AF: 0.534 AC: 1859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	17
DANN	Benign	0.57
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1517527; hg19: chr2-206544302;