rs1878224

Variant names:

• chr12-38915912-T-C
• rs1878224

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 0.0744 in 152,228 control chromosomes in the GnomAD database, including 471 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 0.074 (471 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 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: 0.0743 AC: 11306 AN: 152110 Hom.: 471 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0507

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.0806

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.0346

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0571

Gnomad OTH AF: 0.0766

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

GnomAD4 genome AF: 0.0744 AC: 11325 AN: 152228 Hom.: 471 Cov.: 32 AF XY: 0.0730 AC XY: 5434 AN XY: 74446

African (AFR) AF: 0.125 AC: 5177 AN: 41528

American (AMR) AF: 0.0507 AC: 775 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3472

East Asian (EAS) AF: 0.0808 AC: 418 AN: 5176

South Asian (SAS) AF: 0.0670 AC: 323 AN: 4824

European-Finnish (FIN) AF: 0.0346 AC: 367 AN: 10610

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0571 AC: 3884 AN: 68008

Other (OTH) AF: 0.0758 AC: 160 AN: 2112

Alfa AF: 0.0627 Hom.: 1009

Bravo AF: 0.0774

Asia WGS AF: 0.0860 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.45
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1878224; hg19: chr12-39309714;