chr1-162059501-C-T

Variant names:

• chr1-162059501-C-T
• rs7550692

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 0.402 in 150,708 control chromosomes in the GnomAD database, including 12,872 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 0.40 (12872 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.823

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.63 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: 0.402 AC: 60596 AN: 150588 Hom.: 12873 Cov.: 29

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.402 AC: 60619 AN: 150708 Hom.: 12872 Cov.: 29 AF XY: 0.407 AC XY: 29943 AN XY: 73556

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.397

Alfa AF: 0.354 Hom.: 11634

Bravo AF: 0.402

Asia WGS AF: 0.589 AC: 2047 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7550692; hg19: chr1-162029291;