chr1-162068066-A-G

Variant names:

• chr1-162068066-A-G
• rs10753746

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 0.359 in 152,066 control chromosomes in the GnomAD database, including 10,341 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 0.36 (10341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.61 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: 0.359 AC: 54479 AN: 151948 Hom.: 10326 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.359 AC: 54529 AN: 152066 Hom.: 10341 Cov.: 32 AF XY: 0.365 AC XY: 27143 AN XY: 74326

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.349

Alfa AF: 0.309 Hom.: 7413

Bravo AF: 0.352

Asia WGS AF: 0.583 AC: 2026 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10753746; hg19: chr1-162037856;