rs1287948

Positions:

• chr1-226516024-G-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 0.94 in 152,316 control chromosomes in the GnomAD database, including 67,322 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 0.94 (67322 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 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: 0.940 AC: 143063 AN: 152198 Hom.: 67267 Cov.: 33

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.940 AC: 143180 AN: 152316 Hom.: 67322 Cov.: 33 AF XY: 0.941 AC XY: 70073 AN XY: 74474

Gnomad4 AFR AF: 0.940

Gnomad4 AMR AF: 0.955

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.946

Gnomad4 NFE AF: 0.937

Gnomad4 OTH AF: 0.938

Alfa AF: 0.944 Hom.: 8513

Bravo AF: 0.940

Asia WGS AF: 0.947 AC: 3294 AN: 3478

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	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1287948; hg19: chr1-226703725;