rs2060040

Positions:

• chr2-67736113-G-A

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 0.75 in 152,094 control chromosomes in the GnomAD database, including 42,987 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 0.75 (42987 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.750 AC: 114002 AN: 151976 Hom.: 42951 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.750 AC: 114095 AN: 152094 Hom.: 42987 Cov.: 31 AF XY: 0.753 AC XY: 56012 AN XY: 74352

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.848

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.775

Alfa AF: 0.747 Hom.: 5282

Bravo AF: 0.749

Asia WGS AF: 0.819 AC: 2849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2060040; hg19: chr2-67963245;