rs155908

Positions:

• chr1-189604414-G-A

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 0.559 in 151,790 control chromosomes in the GnomAD database, including 24,886 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 (24886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84762 AN: 151674 Hom.: 24856 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.559 AC: 84838 AN: 151790 Hom.: 24886 Cov.: 32 AF XY: 0.554 AC XY: 41105 AN XY: 74148

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.528

Alfa AF: 0.532 Hom.: 2750

Bravo AF: 0.562

Asia WGS AF: 0.436 AC: 1513 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.083
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs155908; hg19: chr1-189573544;