2-240055848-C-G

Variant names:

• chr2-240055848-C-G
• rs12471078

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 0.61 in 152,060 control chromosomes in the GnomAD database, including 30,445 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 0.61 (30445 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 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: 0.609 AC: 92584 AN: 151942 Hom.: 30392 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.610 AC: 92687 AN: 152060 Hom.: 30445 Cov.: 32 AF XY: 0.614 AC XY: 45630 AN XY: 74316

African (AFR) AF: 0.861 AC: 35753 AN: 41514

American (AMR) AF: 0.609 AC: 9315 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1432 AN: 3466

East Asian (EAS) AF: 0.737 AC: 3792 AN: 5148

South Asian (SAS) AF: 0.592 AC: 2860 AN: 4828

European-Finnish (FIN) AF: 0.528 AC: 5571 AN: 10552

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.475 AC: 32245 AN: 67950

Other (OTH) AF: 0.586 AC: 1238 AN: 2112

Alfa AF: 0.560 Hom.: 3138

Bravo AF: 0.623

Asia WGS AF: 0.654 AC: 2270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.19
DANN	Benign	0.50
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12471078; hg19: chr2-240995265;