chr1-159248476-A-C

Position:

• chr1-159248476-A-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 0.561 in 152,068 control chromosomes in the GnomAD database, including 26,982 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 (26982 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 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: 0.561 AC: 85181 AN: 151948 Hom.: 26933 Cov.: 32

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.561 AC: 85286 AN: 152068 Hom.: 26982 Cov.: 32 AF XY: 0.558 AC XY: 41494 AN XY: 74322

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.517

Alfa AF: 0.429 Hom.: 30206

Bravo AF: 0.580

Asia WGS AF: 0.485 AC: 1687 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3845624; hg19: chr1-159218266;