chr2-60639691-G-A

Position:

• chr2-60639691-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 0.356 in 152,056 control chromosomes in the GnomAD database, including 10,579 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 0.36 (10579 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54059 AN: 151938 Hom.: 10549 Cov.: 33

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.356 AC: 54136 AN: 152056 Hom.: 10579 Cov.: 33 AF XY: 0.349 AC XY: 25960 AN XY: 74312

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.327

Alfa AF: 0.314 Hom.: 3605

Bravo AF: 0.367

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.90
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1866206; hg19: chr2-60866826;