2-27525757-A-G

Variant names:

• chr2-27525757-A-G
• rs1260333

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 0.58 in 142,650 control chromosomes in the GnomAD database, including 24,634 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 0.58 (24634 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 70 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.688 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: 0.580 AC: 82643 AN: 142604 Hom.: 24603 Cov.: 22

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.580 AC: 82709 AN: 142650 Hom.: 24634 Cov.: 22 AF XY: 0.581 AC XY: 39942 AN XY: 68722

African (AFR) AF: 0.665 AC: 25357 AN: 38128

American (AMR) AF: 0.559 AC: 7920 AN: 14174

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1502 AN: 3434

East Asian (EAS) AF: 0.500 AC: 2419 AN: 4834

South Asian (SAS) AF: 0.709 AC: 3197 AN: 4510

European-Finnish (FIN) AF: 0.575 AC: 4621 AN: 8034

Middle Eastern (MID) AF: 0.448 AC: 128 AN: 286

European-Non Finnish (NFE) AF: 0.544 AC: 36064 AN: 66354

Other (OTH) AF: 0.523 AC: 1046 AN: 2000

Alfa AF: 0.557 Hom.: 52632

Bravo AF: 0.581

Asia WGS AF: 0.630 AC: 2012 AN: 3200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.6
DANN	Benign	0.61
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs1260333; hg19: chr2-27748624;