chr2-61700965-A-C

Position:

• chr2-61700965-A-C

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 0.863 in 152,202 control chromosomes in the GnomAD database, including 56,714 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 0.86 (56714 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 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: 0.862 AC: 131152 AN: 152084 Hom.: 56645 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.856

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

GnomAD4 genome AF: 0.863 AC: 131282 AN: 152202 Hom.: 56714 Cov.: 32 AF XY: 0.866 AC XY: 64465 AN XY: 74418

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.902

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.933

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.857

Alfa AF: 0.863 Hom.: 76758

Bravo AF: 0.860

Asia WGS AF: 0.912 AC: 3168 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4672448; hg19: chr2-61928100;