chr10-99856822-A-G

Variant names:

• chr10-99856822-A-G
• rs7067971

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 0.326 in 152,182 control chromosomes in the GnomAD database, including 8,483 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 0.33 (8483 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.369 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: 0.326 AC: 49525 AN: 152064 Hom.: 8491 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.326 AC: 49538 AN: 152182 Hom.: 8483 Cov.: 33 AF XY: 0.324 AC XY: 24133 AN XY: 74382

African (AFR) AF: 0.243 AC: 10070 AN: 41516

American (AMR) AF: 0.346 AC: 5295 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1233 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1194 AN: 5180

South Asian (SAS) AF: 0.323 AC: 1562 AN: 4830

European-Finnish (FIN) AF: 0.336 AC: 3557 AN: 10584

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25333 AN: 67994

Other (OTH) AF: 0.345 AC: 728 AN: 2112

Alfa AF: 0.358 Hom.: 32322

Bravo AF: 0.321

Asia WGS AF: 0.270 AC: 940 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	5.1
DANN	Benign	0.45
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs7067971; hg19: chr10-101616579;