rs310850

Variant names:

• chr12-77088108-A-G
• rs310850

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 0.467 in 151,956 control chromosomes in the GnomAD database, including 17,993 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 (17993 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 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: 0.467 AC: 70898 AN: 151838 Hom.: 17964 Cov.: 32

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.467 AC: 70975 AN: 151956 Hom.: 17993 Cov.: 32 AF XY: 0.455 AC XY: 33801 AN XY: 74240

African (AFR) AF: 0.665 AC: 27548 AN: 41454

American (AMR) AF: 0.358 AC: 5468 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1505 AN: 3466

East Asian (EAS) AF: 0.170 AC: 876 AN: 5166

South Asian (SAS) AF: 0.282 AC: 1357 AN: 4812

European-Finnish (FIN) AF: 0.379 AC: 3993 AN: 10526

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.424 AC: 28797 AN: 67964

Other (OTH) AF: 0.474 AC: 1002 AN: 2112

Alfa AF: 0.453 Hom.: 25965

Bravo AF: 0.476

Asia WGS AF: 0.298 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.2
DANN	Benign	0.67
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs310850; hg19: chr12-77481888;