rs77724872

Variant names:

• chr12-104360722-C-T
• rs77724872

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0448 in 152,270 control chromosomes in the GnomAD database, including 159 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 0.045 (159 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0448 (6816/152270) while in subpopulation AMR AF = 0.0529 (809/15296). AF 95% confidence interval is 0.0499. There are 159 homozygotes in GnomAd4. There are 3327 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 159 gene

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: 0.0447 AC: 6800 AN: 152152 Hom.: 159 Cov.: 32

Gnomad AFR AF: 0.0395

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0530

Gnomad ASJ AF: 0.0692

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.0424

Gnomad FIN AF: 0.0280

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0505

Gnomad OTH AF: 0.0451

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

GnomAD4 genome AF: 0.0448 AC: 6816 AN: 152270 Hom.: 159 Cov.: 32 AF XY: 0.0447 AC XY: 3327 AN XY: 74458

African (AFR) AF: 0.0397 AC: 1648 AN: 41550

American (AMR) AF: 0.0529 AC: 809 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0692 AC: 240 AN: 3470

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5182

South Asian (SAS) AF: 0.0435 AC: 210 AN: 4826

European-Finnish (FIN) AF: 0.0280 AC: 297 AN: 10602

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0505 AC: 3435 AN: 68030

Other (OTH) AF: 0.0446 AC: 94 AN: 2108

Alfa AF: 0.0440 Hom.: 33

Bravo AF: 0.0461

Asia WGS AF: 0.0440 AC: 153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.42
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs77724872; hg19: chr12-104754500;