12-57655536-C-G

Variant names:

• chr12-57655536-C-G
• rs1678520

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 0.6 in 152,186 control chromosomes in the GnomAD database, including 27,976 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 0.60 (27976 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 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: 0.600 AC: 91217 AN: 152066 Hom.: 27966 Cov.: 33

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.600 AC: 91275 AN: 152186 Hom.: 27976 Cov.: 33 AF XY: 0.593 AC XY: 44155 AN XY: 74412

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.639

Alfa AF: 0.502 Hom.: 1419

Bravo AF: 0.600

Asia WGS AF: 0.461 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.40
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1678520; hg19: chr12-58049319;