2-78312540-G-A

Variant names:

• chr2-78312540-G-A
• rs2037723

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 0.0896 in 152,096 control chromosomes in the GnomAD database, including 749 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 0.090 (749 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0895 AC: 13605 AN: 151978 Hom.: 747 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0442

Gnomad ASJ AF: 0.0786

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0948

Gnomad FIN AF: 0.0960

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0634

Gnomad OTH AF: 0.0775

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

GnomAD4 genome AF: 0.0896 AC: 13623 AN: 152096 Hom.: 749 Cov.: 32 AF XY: 0.0892 AC XY: 6637 AN XY: 74370

African (AFR) AF: 0.147 AC: 6095 AN: 41470

American (AMR) AF: 0.0441 AC: 673 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0786 AC: 273 AN: 3472

East Asian (EAS) AF: 0.113 AC: 586 AN: 5174

South Asian (SAS) AF: 0.0951 AC: 458 AN: 4818

European-Finnish (FIN) AF: 0.0960 AC: 1016 AN: 10582

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0634 AC: 4308 AN: 67990

Other (OTH) AF: 0.0758 AC: 160 AN: 2112

Alfa AF: 0.0728 Hom.: 224

Bravo AF: 0.0878

Asia WGS AF: 0.108 AC: 373 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.65
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs2037723; hg19: chr2-78539666;