rs7038622

Variant names:

• chr9-126843646-G-A
• rs7038622

Your query was ambiguous. Multiple possible variants found:

• chr9-126843646-G-A
• chr9-126843646-G-C

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 0.139 in 151,040 control chromosomes in the GnomAD database, including 3,972 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 0.14 (3972 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.139 AC: 20904 AN: 150922 Hom.: 3958 Cov.: 31

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0715

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.00991

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00265

Gnomad OTH AF: 0.0983

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

GnomAD4 genome AF: 0.139 AC: 20954 AN: 151040 Hom.: 3972 Cov.: 31 AF XY: 0.139 AC XY: 10211 AN XY: 73616

African (AFR) AF: 0.412 AC: 16899 AN: 41060

American (AMR) AF: 0.0713 AC: 1083 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.0219 AC: 76 AN: 3464

East Asian (EAS) AF: 0.370 AC: 1894 AN: 5124

South Asian (SAS) AF: 0.106 AC: 509 AN: 4802

European-Finnish (FIN) AF: 0.00991 AC: 101 AN: 10188

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00265 AC: 180 AN: 67916

Other (OTH) AF: 0.0991 AC: 208 AN: 2098

Alfa AF: 0.0491 Hom.: 759

Bravo AF: 0.158

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.6
DANN	Benign	0.67
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs7038622; hg19: chr9-129605925;