rs7090530

chr10-6068912-C-Achr10-6068912-C-T

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 0.595 in 152,004 control chromosomes in the GnomAD database, including 27,250 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 0.59 (27250 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 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: 0.595 AC: 90338 AN: 151886 Hom.: 27229 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.595 AC: 90397 AN: 152004 Hom.: 27250 Cov.: 32 AF XY: 0.599 AC XY: 44484 AN XY: 74306

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.570

Alfa AF: 0.585 Hom.: 33749

Bravo AF: 0.587

Asia WGS AF: 0.695 AC: 2421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.46
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7090530; hg19: chr10-6110875;