rs12068753

Positions:

• chr1-159722747-T-A
• chr1-159722747-T-C

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 0.146 in 152,170 control chromosomes in the GnomAD database, including 2,757 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 0.15 (2757 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 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: 0.146 AC: 22150 AN: 152052 Hom.: 2745 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0804

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.146 AC: 22194 AN: 152170 Hom.: 2757 Cov.: 32 AF XY: 0.144 AC XY: 10735 AN XY: 74404

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.0803

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0653

Gnomad4 NFE AF: 0.0614

Gnomad4 OTH AF: 0.137

Alfa AF: 0.105 Hom.: 206

Bravo AF: 0.154

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12068753; hg19: chr1-159692537;