chr7-21250138-G-A

Variant names:

• chr7-21250138-G-A
• rs10236032

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 0.693 in 152,138 control chromosomes in the GnomAD database, including 37,013 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 0.69 (37013 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.976
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 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: 0.693 AC: 105282 AN: 152020 Hom.: 36989 Cov.: 34

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.693 AC: 105364 AN: 152138 Hom.: 37013 Cov.: 34 AF XY: 0.690 AC XY: 51304 AN XY: 74366

African (AFR) AF: 0.604 AC: 25047 AN: 41500

American (AMR) AF: 0.722 AC: 11029 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2858 AN: 3468

East Asian (EAS) AF: 0.470 AC: 2430 AN: 5166

South Asian (SAS) AF: 0.602 AC: 2902 AN: 4820

European-Finnish (FIN) AF: 0.733 AC: 7772 AN: 10602

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50920 AN: 67990

Other (OTH) AF: 0.725 AC: 1532 AN: 2114

Alfa AF: 0.736 Hom.: 65855

Bravo AF: 0.698

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.30
DANN	Benign	0.67
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs10236032; hg19: chr7-21289757;