rs2037723

Variant names:

• chr2-78312540-G-A
• rs2037723

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 0.0896 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0895 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

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.0441

Gnomad4 ASJ AF: 0.0786

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0951

Gnomad4 FIN AF: 0.0960

Gnomad4 NFE AF: 0.0634

Gnomad4 OTH AF: 0.0758

Alfa AF: 0.0735 Hom.: 201

Bravo AF: 0.0878

Asia WGS AF: 0.108 AC: 373 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2037723; hg19: chr2-78539666;