12-77103301-C-G

Variant names:

• chr12-77103301-C-G
• rs10506728

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 0.16 in 151,994 control chromosomes in the GnomAD database, including 2,030 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 0.16 (2030 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24249 AN: 151876 Hom.: 2027 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.160 AC: 24246 AN: 151994 Hom.: 2030 Cov.: 31 AF XY: 0.165 AC XY: 12238 AN XY: 74278

African (AFR) AF: 0.137 AC: 5684 AN: 41464

American (AMR) AF: 0.137 AC: 2084 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3470

East Asian (EAS) AF: 0.247 AC: 1271 AN: 5156

South Asian (SAS) AF: 0.250 AC: 1204 AN: 4814

European-Finnish (FIN) AF: 0.209 AC: 2209 AN: 10554

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10547 AN: 67962

Other (OTH) AF: 0.160 AC: 338 AN: 2110

Alfa AF: 0.146 Hom.: 209

Bravo AF: 0.155

Asia WGS AF: 0.222 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30
DANN	Benign	0.61
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10506728; hg19: chr12-77497081;