2-240713286-T-C

Variant names:

• chr2-240713286-T-C
• rs755300

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 0.457 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.657 AC: 27255 AN: 41504

American (AMR) AF: 0.514 AC: 7862 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1859 AN: 3472

East Asian (EAS) AF: 0.235 AC: 1217 AN: 5174

South Asian (SAS) AF: 0.216 AC: 1043 AN: 4820

European-Finnish (FIN) AF: 0.383 AC: 4062 AN: 10604

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24720 AN: 67952

Other (OTH) AF: 0.458 AC: 965 AN: 2108

Alfa AF: 0.393 Hom.: 41149

Bravo AF: 0.481

Asia WGS AF: 0.271 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.14
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs755300; hg19: chr2-241652703;