10-68259614-G-A

Variant names:

• chr10-68259614-G-A
• rs12571093

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 0.139 in 152,038 control chromosomes in the GnomAD database, including 1,955 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 0.14 (1955 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 30 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.231 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: 0.139 AC: 21076 AN: 151920 Hom.: 1954 Cov.: 31

Gnomad AFR AF: 0.0314

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.139 AC: 21085 AN: 152038 Hom.: 1955 Cov.: 31 AF XY: 0.144 AC XY: 10690 AN XY: 74316

African (AFR) AF: 0.0313 AC: 1299 AN: 41492

American (AMR) AF: 0.213 AC: 3259 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 775 AN: 3470

East Asian (EAS) AF: 0.150 AC: 776 AN: 5178

South Asian (SAS) AF: 0.243 AC: 1169 AN: 4814

European-Finnish (FIN) AF: 0.201 AC: 2114 AN: 10526

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11099 AN: 67970

Other (OTH) AF: 0.143 AC: 301 AN: 2110

Alfa AF: 0.157 Hom.: 6488

Bravo AF: 0.136

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.68
DANN	Benign	0.56
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs12571093; hg19: chr10-70019371;