chr10-6068912-C-A

Variant names:

• chr10-6068912-C-A
• rs7090530

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 0.595 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
• Publications: 44 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.549 AC: 22749 AN: 41432

American (AMR) AF: 0.628 AC: 9600 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1535 AN: 3470

East Asian (EAS) AF: 0.696 AC: 3598 AN: 5170

South Asian (SAS) AF: 0.661 AC: 3184 AN: 4820

European-Finnish (FIN) AF: 0.667 AC: 7034 AN: 10552

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40842 AN: 67968

Other (OTH) AF: 0.570 AC: 1203 AN: 2110

Alfa AF: 0.585 Hom.: 42963

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
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs7090530; hg19: chr10-6110875;