12-57655536-C-G

Variant names:

• chr12-57655536-C-G
• rs1678520

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 0.6 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
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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

African (AFR) AF: 0.514 AC: 21312 AN: 41500

American (AMR) AF: 0.641 AC: 9805 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2395 AN: 3472

East Asian (EAS) AF: 0.373 AC: 1928 AN: 5174

South Asian (SAS) AF: 0.471 AC: 2278 AN: 4834

European-Finnish (FIN) AF: 0.594 AC: 6288 AN: 10592

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45263 AN: 68002

Other (OTH) AF: 0.639 AC: 1351 AN: 2114

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
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs1678520; hg19: chr12-58049319;