2-201370625-A-G

Variant names:

• chr2-201370625-A-G
• rs7578456

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 0.575 in 152,008 control chromosomes in the GnomAD database, including 25,534 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 0.58 (25534 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87355 AN: 151890 Hom.: 25517 Cov.: 31

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.575 AC: 87410 AN: 152008 Hom.: 25534 Cov.: 31 AF XY: 0.576 AC XY: 42828 AN XY: 74300

African (AFR) AF: 0.551 AC: 22835 AN: 41450

American (AMR) AF: 0.471 AC: 7200 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1910 AN: 3470

East Asian (EAS) AF: 0.735 AC: 3781 AN: 5142

South Asian (SAS) AF: 0.785 AC: 3782 AN: 4818

European-Finnish (FIN) AF: 0.567 AC: 5996 AN: 10574

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40153 AN: 67954

Other (OTH) AF: 0.535 AC: 1132 AN: 2114

Alfa AF: 0.595 Hom.: 21956

Bravo AF: 0.562

Asia WGS AF: 0.760 AC: 2641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7578456; hg19: chr2-202235348;