rs2060040

Variant names:

• chr2-67736113-G-A
• rs2060040

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 0.75 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.666 AC: 27616 AN: 41482

American (AMR) AF: 0.827 AC: 12642 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.848 AC: 2938 AN: 3466

East Asian (EAS) AF: 0.838 AC: 4336 AN: 5176

South Asian (SAS) AF: 0.789 AC: 3795 AN: 4810

European-Finnish (FIN) AF: 0.792 AC: 8383 AN: 10588

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.761 AC: 51732 AN: 67968

Other (OTH) AF: 0.775 AC: 1635 AN: 2110

Alfa AF: 0.744 Hom.: 5452

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
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs2060040; hg19: chr2-67963245;