chr2-85945151-A-G

Variant names:

• chr2-85945151-A-G
• rs1370699

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 0.651 in 152,100 control chromosomes in the GnomAD database, including 33,403 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 0.65 (33403 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.726 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: 0.651 AC: 98951 AN: 151982 Hom.: 33382 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.651 AC: 99017 AN: 152100 Hom.: 33403 Cov.: 32 AF XY: 0.653 AC XY: 48559 AN XY: 74354

African (AFR) AF: 0.456 AC: 18907 AN: 41446

American (AMR) AF: 0.729 AC: 11142 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2557 AN: 3472

East Asian (EAS) AF: 0.625 AC: 3235 AN: 5172

South Asian (SAS) AF: 0.705 AC: 3400 AN: 4820

European-Finnish (FIN) AF: 0.731 AC: 7749 AN: 10596

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49705 AN: 67994

Other (OTH) AF: 0.671 AC: 1419 AN: 2114

Alfa AF: 0.705 Hom.: 126933

Bravo AF: 0.644

Asia WGS AF: 0.644 AC: 2241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.71
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs1370699; hg19: chr2-86172274;