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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.139 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

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.0713

Gnomad4 ASJ AF: 0.0219

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.00991

Gnomad4 NFE AF: 0.00265

Gnomad4 OTH AF: 0.0991

Alfa AF: 0.0479 Hom.: 483

Bravo AF: 0.158

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7038622; hg19: chr9-129605925;