12-60110401-T-G

Variant names:

• chr12-60110401-T-G
• rs1154720

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 0.895 in 152,084 control chromosomes in the GnomAD database, including 62,358 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 0.90 (62358 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.895 AC: 136066 AN: 151966 Hom.: 62342 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.952

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.994

Gnomad FIN AF: 0.986

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.895 AC: 136126 AN: 152084 Hom.: 62358 Cov.: 32 AF XY: 0.898 AC XY: 66788 AN XY: 74342

African (AFR) AF: 0.672 AC: 27852 AN: 41430

American (AMR) AF: 0.952 AC: 14510 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3363 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5172 AN: 5172

South Asian (SAS) AF: 0.994 AC: 4790 AN: 4818

European-Finnish (FIN) AF: 0.986 AC: 10470 AN: 10622

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.982 AC: 66809 AN: 68012

Other (OTH) AF: 0.935 AC: 1973 AN: 2110

Alfa AF: 0.911 Hom.: 10823

Bravo AF: 0.883

Asia WGS AF: 0.972 AC: 3380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs1154720; hg19: chr12-60504182;