chr10-36670379-A-G

Position:

• chr10-36670379-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 0.473 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.447

Alfa AF: 0.399 Hom.: 1702

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10827687; hg19: chr10-36959307;