10-77647212-C-G

Variant names:

• chr10-77647212-C-G
• rs2812415

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 0.779 in 152,112 control chromosomes in the GnomAD database, including 46,717 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 0.78 (46717 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

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 (AFR) allele frequency at 95% confidence interval = 0.893 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: 0.779 AC: 118412 AN: 151994 Hom.: 46665 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.779 AC: 118518 AN: 152112 Hom.: 46717 Cov.: 32 AF XY: 0.781 AC XY: 58103 AN XY: 74360

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.801

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.777

Alfa AF: 0.645 Hom.: 1723

Bravo AF: 0.783

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2812415; hg19: chr10-79406970;