chr1-157440899-C-G

Position:

• chr1-157440899-C-G

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 0.284 in 152,094 control chromosomes in the GnomAD database, including 6,722 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 0.28 (6722 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 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: 0.284 AC: 43216 AN: 151974 Hom.: 6725 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0637

Gnomad SAS AF: 0.0975

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.284 AC: 43230 AN: 152094 Hom.: 6722 Cov.: 32 AF XY: 0.281 AC XY: 20856 AN XY: 74342

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.0641

Gnomad4 SAS AF: 0.0976

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.305

Alfa AF: 0.171 Hom.: 368

Bravo AF: 0.290

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.27
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2309879; hg19: chr1-157410689;