rs7072263

Variant names:

• chr10-99607888-G-A
• rs7072263

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 0.242 in 152,084 control chromosomes in the GnomAD database, including 4,613 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 0.24 (4613 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 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: 0.242 AC: 36784 AN: 151966 Hom.: 4614 Cov.: 34

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.242 AC: 36801 AN: 152084 Hom.: 4613 Cov.: 34 AF XY: 0.241 AC XY: 17929 AN XY: 74364

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.208

Alfa AF: 0.262 Hom.: 5106

Bravo AF: 0.232

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7072263; hg19: chr10-101367645;