rs12048904

Variant names:

• chr1-100865980-T-C
• rs12048904

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 0.485 in 152,060 control chromosomes in the GnomAD database, including 19,554 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 0.48 (19554 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646
• Publications: 25 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 = 0.596 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: 0.485 AC: 73705 AN: 151942 Hom.: 19556 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.485 AC: 73726 AN: 152060 Hom.: 19554 Cov.: 32 AF XY: 0.482 AC XY: 35814 AN XY: 74308

African (AFR) AF: 0.270 AC: 11209 AN: 41504

American (AMR) AF: 0.472 AC: 7204 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2222 AN: 3468

East Asian (EAS) AF: 0.394 AC: 2029 AN: 5156

South Asian (SAS) AF: 0.540 AC: 2604 AN: 4824

European-Finnish (FIN) AF: 0.555 AC: 5863 AN: 10558

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40821 AN: 67980

Other (OTH) AF: 0.488 AC: 1030 AN: 2110

Alfa AF: 0.569 Hom.: 80378

Bravo AF: 0.465

Asia WGS AF: 0.425 AC: 1482 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	0.091
DANN	Benign	0.63
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs12048904; hg19: chr1-101331536;