rs755302

Variant names:

• chr2-240712978-G-A
• rs755302

Your query was ambiguous. Multiple possible variants found:

• chr2-240712978-G-A
• chr2-240712978-G-C

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 0.197 in 152,016 control chromosomes in the GnomAD database, including 3,684 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 (3684 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.265 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: 0.197 AC: 29921 AN: 151914 Hom.: 3686 Cov.: 32

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0870

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.197 AC: 29911 AN: 152016 Hom.: 3684 Cov.: 32 AF XY: 0.193 AC XY: 14301 AN XY: 74290

African (AFR) AF: 0.0846 AC: 3504 AN: 41440

American (AMR) AF: 0.200 AC: 3063 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1404 AN: 3468

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5174

South Asian (SAS) AF: 0.0876 AC: 422 AN: 4820

European-Finnish (FIN) AF: 0.240 AC: 2533 AN: 10550

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18212 AN: 67966

Other (OTH) AF: 0.227 AC: 480 AN: 2112

Alfa AF: 0.242 Hom.: 9009

Bravo AF: 0.193

Asia WGS AF: 0.0480 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.59
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs755302; hg19: chr2-241652395;