rs7038622

chr9-126843646-G-Achr9-126843646-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;