chr10-29807699-A-G

Variant names:

• chr10-29807699-A-G
• rs2986971

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 0.487 in 152,052 control chromosomes in the GnomAD database, including 18,295 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 0.49 (18295 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 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: 0.487 AC: 73937 AN: 151934 Hom.: 18287 Cov.: 31

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.487 AC: 73982 AN: 152052 Hom.: 18295 Cov.: 31 AF XY: 0.478 AC XY: 35558 AN XY: 74330

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.520

Alfa AF: 0.490 Hom.: 42694

Bravo AF: 0.496

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2986971; hg19: chr10-30096628;