10-36670379-A-G

Variant names:

• chr10-36670379-A-G
• rs10827687

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 0.473 in 152,066 control chromosomes in the GnomAD database, including 17,462 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 0.47 (17462 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 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: 0.473 AC: 71927 AN: 151944 Hom.: 17456 Cov.: 33

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.473 AC: 71961 AN: 152066 Hom.: 17462 Cov.: 33 AF XY: 0.471 AC XY: 35029 AN XY: 74330

African (AFR) AF: 0.527 AC: 21876 AN: 41506

American (AMR) AF: 0.412 AC: 6296 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1584 AN: 3468

East Asian (EAS) AF: 0.140 AC: 724 AN: 5160

South Asian (SAS) AF: 0.374 AC: 1799 AN: 4814

European-Finnish (FIN) AF: 0.570 AC: 6010 AN: 10552

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32178 AN: 67972

Other (OTH) AF: 0.447 AC: 944 AN: 2112

Alfa AF: 0.403 Hom.: 1809

Bravo AF: 0.462

Asia WGS AF: 0.261 AC: 912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.23
DANN	Benign	0.29
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs10827687; hg19: chr10-36959307;