rs12081765

Positions:

• chr1-165372612-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 0.558 in 152,014 control chromosomes in the GnomAD database, including 23,971 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 0.56 (23971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84779 AN: 151896 Hom.: 23954 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.558 AC: 84842 AN: 152014 Hom.: 23971 Cov.: 32 AF XY: 0.556 AC XY: 41321 AN XY: 74306

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.526

Alfa AF: 0.551 Hom.: 34934

Bravo AF: 0.551

Asia WGS AF: 0.389 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12081765; hg19: chr1-165341849;