rs2317230

Positions:

• chr1-157705207-G-T

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 0.552 in 152,084 control chromosomes in the GnomAD database, including 26,198 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 0.55 (26198 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644

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 (AFR) allele frequency at 95% confidence interval = 0.865 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: 0.551 AC: 83788 AN: 151966 Hom.: 26139 Cov.: 32

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.552 AC: 83898 AN: 152084 Hom.: 26198 Cov.: 32 AF XY: 0.547 AC XY: 40661 AN XY: 74352

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.520

Alfa AF: 0.484 Hom.: 2519

Bravo AF: 0.571

Asia WGS AF: 0.502 AC: 1747 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	0.80
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2317230; hg19: chr1-157674997;