rs755300

Variant names:

• chr2-240713286-T-C
• rs755300

Your query was ambiguous. Multiple possible variants found:

• chr2-240713286-T-C
• chr2-240713286-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.457 in 152,132 control chromosomes in the GnomAD database, including 17,377 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 0.46 (17377 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 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: 0.456 AC: 69387 AN: 152014 Hom.: 17345 Cov.: 33

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.457 AC: 69471 AN: 152132 Hom.: 17377 Cov.: 33 AF XY: 0.454 AC XY: 33786 AN XY: 74378

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.458

Alfa AF: 0.379 Hom.: 15676

Bravo AF: 0.481

Asia WGS AF: 0.271 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs755300; hg19: chr2-241652703;