chr2-207637006-A-G

Variant names:

• chr2-207637006-A-G
• rs7591784

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 0.478 in 151,468 control chromosomes in the GnomAD database, including 17,437 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 0.48 (17437 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72416 AN: 151350 Hom.: 17424 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.478 AC: 72463 AN: 151468 Hom.: 17437 Cov.: 31 AF XY: 0.480 AC XY: 35473 AN XY: 73968

African (AFR) AF: 0.510 AC: 21066 AN: 41300

American (AMR) AF: 0.472 AC: 7186 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1795 AN: 3470

East Asian (EAS) AF: 0.607 AC: 3102 AN: 5114

South Asian (SAS) AF: 0.426 AC: 2052 AN: 4818

European-Finnish (FIN) AF: 0.473 AC: 4958 AN: 10478

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.454 AC: 30761 AN: 67778

Other (OTH) AF: 0.502 AC: 1055 AN: 2100

Alfa AF: 0.468 Hom.: 71913

Bravo AF: 0.481

Asia WGS AF: 0.518 AC: 1799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.74
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs7591784; hg19: chr2-208501730;