12-60416871-T-C

Variant names:

• chr12-60416871-T-C
• rs2655898

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 0.339 in 151,958 control chromosomes in the GnomAD database, including 10,075 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 0.34 (10075 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 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: 0.339 AC: 51508 AN: 151840 Hom.: 10066 Cov.: 33

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.339 AC: 51570 AN: 151958 Hom.: 10075 Cov.: 33 AF XY: 0.337 AC XY: 25004 AN XY: 74254

African (AFR) AF: 0.545 AC: 22601 AN: 41442

American (AMR) AF: 0.266 AC: 4059 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1263 AN: 3470

East Asian (EAS) AF: 0.324 AC: 1676 AN: 5172

South Asian (SAS) AF: 0.232 AC: 1120 AN: 4828

European-Finnish (FIN) AF: 0.270 AC: 2853 AN: 10558

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16980 AN: 67904

Other (OTH) AF: 0.329 AC: 693 AN: 2108

Alfa AF: 0.286 Hom.: 20010

Bravo AF: 0.348

Asia WGS AF: 0.254 AC: 881 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.64
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2655898; hg19: chr12-60810652;