rs12021510

chr1-161739421-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00989

Gnomad4 AMR AF: 0.0417

Gnomad4 ASJ AF: 0.0176

Gnomad4 EAS AF: 0.0718

Gnomad4 SAS AF: 0.0315

Gnomad4 FIN AF: 0.0223

Gnomad4 NFE AF: 0.0576

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0537 Hom.: 205

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12021510; hg19: chr1-161709211;