rs10877839

Variant names:

• chr12-62424701-T-C
• rs10877839

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 0.266 in 152,058 control chromosomes in the GnomAD database, including 6,638 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 0.27 (6638 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.933
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40456 AN: 151942 Hom.: 6631 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.266 AC: 40463 AN: 152058 Hom.: 6638 Cov.: 32 AF XY: 0.274 AC XY: 20395 AN XY: 74332

African (AFR) AF: 0.0874 AC: 3628 AN: 41532

American (AMR) AF: 0.311 AC: 4756 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1185 AN: 3472

East Asian (EAS) AF: 0.443 AC: 2286 AN: 5166

South Asian (SAS) AF: 0.218 AC: 1053 AN: 4820

European-Finnish (FIN) AF: 0.481 AC: 5068 AN: 10546

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21737 AN: 67936

Other (OTH) AF: 0.247 AC: 521 AN: 2106

Alfa AF: 0.301 Hom.: 32120

Bravo AF: 0.249

Asia WGS AF: 0.300 AC: 1046 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.62
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs10877839; hg19: chr12-62818481;