rs913168

Positions:

• chr1-46392904-T-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 0.414 in 151,728 control chromosomes in the GnomAD database, including 13,244 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 0.41 (13244 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 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: 0.414 AC: 62793 AN: 151610 Hom.: 13209 Cov.: 31

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.414 AC: 62864 AN: 151728 Hom.: 13244 Cov.: 31 AF XY: 0.413 AC XY: 30602 AN XY: 74148

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.415

Alfa AF: 0.415 Hom.: 1196

Bravo AF: 0.409

Asia WGS AF: 0.397 AC: 1382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
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: rs913168; hg19: chr1-46858576;