chr2-85535638-A-G

Position:

• chr2-85535638-A-G

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 0.505 in 151,992 control chromosomes in the GnomAD database, including 20,055 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 0.50 (20055 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 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: 0.505 AC: 76637 AN: 151874 Hom.: 20036 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.505 AC: 76703 AN: 151992 Hom.: 20055 Cov.: 32 AF XY: 0.502 AC XY: 37263 AN XY: 74278

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.506

Alfa AF: 0.468 Hom.: 6996

Bravo AF: 0.507

Asia WGS AF: 0.434 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10179195; hg19: chr2-85762761;