rs7100400

Positions:

• chr10-6082117-A-G

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 0.0349 in 152,176 control chromosomes in the GnomAD database, including 164 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 0.035 (164 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0349 AC: 5314 AN: 152058 Hom.: 163 Cov.: 31

Gnomad AFR AF: 0.00884

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.0313

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.0303

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0349 AC: 5317 AN: 152176 Hom.: 164 Cov.: 31 AF XY: 0.0348 AC XY: 2588 AN XY: 74418

Gnomad4 AFR AF: 0.00881

Gnomad4 AMR AF: 0.0313

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0374

Gnomad4 FIN AF: 0.0303

Gnomad4 NFE AF: 0.0435

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0391 Hom.: 81

Bravo AF: 0.0343

Asia WGS AF: 0.102 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7100400; hg19: chr10-6124080;