rs12021510

Variant names:

• chr1-161739421-A-G
• rs12021510

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 0.0391 in 152,246 control chromosomes in the GnomAD database, including 163 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 0.039 (163 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0658 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: 0.0392 AC: 5963 AN: 152128 Hom.: 164 Cov.: 33

Gnomad AFR AF: 0.00992

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.0718

Gnomad SAS AF: 0.0323

Gnomad FIN AF: 0.0223

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0576

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0391 AC: 5960 AN: 152246 Hom.: 163 Cov.: 33 AF XY: 0.0370 AC XY: 2757 AN XY: 74418

African (AFR) AF: 0.00989 AC: 411 AN: 41564

American (AMR) AF: 0.0417 AC: 638 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3470

East Asian (EAS) AF: 0.0718 AC: 372 AN: 5184

South Asian (SAS) AF: 0.0315 AC: 152 AN: 4822

European-Finnish (FIN) AF: 0.0223 AC: 236 AN: 10588

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.0576 AC: 3915 AN: 68006

Other (OTH) AF: 0.0402 AC: 85 AN: 2112

Alfa AF: 0.0516 Hom.: 309

Bravo AF: 0.0410

Asia WGS AF: 0.0640 AC: 224 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	5.7
DANN	Benign	0.65
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs12021510; hg19: chr1-161709211;