2-5200369-G-A

Variant names:

• chr2-5200369-G-A
• rs6718709

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 0.49 in 151,900 control chromosomes in the GnomAD database, including 19,808 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 0.49 (19808 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 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: 0.490 AC: 74387 AN: 151782 Hom.: 19811 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.490 AC: 74401 AN: 151900 Hom.: 19808 Cov.: 32 AF XY: 0.499 AC XY: 37048 AN XY: 74242

African (AFR) AF: 0.302 AC: 12493 AN: 41424

American (AMR) AF: 0.501 AC: 7637 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2358 AN: 3470

East Asian (EAS) AF: 0.933 AC: 4814 AN: 5160

South Asian (SAS) AF: 0.606 AC: 2919 AN: 4818

European-Finnish (FIN) AF: 0.631 AC: 6648 AN: 10542

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.525 AC: 35646 AN: 67924

Other (OTH) AF: 0.523 AC: 1101 AN: 2106

Alfa AF: 0.510 Hom.: 58344

Bravo AF: 0.474

Asia WGS AF: 0.732 AC: 2541 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	0.026
DANN	Benign	0.66
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6718709; hg19: chr2-5340502;