rs4657270

Positions:

• chr1-163408857-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 0.0437 in 152,218 control chromosomes in the GnomAD database, including 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 0.044 (198 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0601 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: 0.0438 AC: 6661 AN: 152100 Hom.: 198 Cov.: 33

Gnomad AFR AF: 0.00997

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0407

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.0333

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0798

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0617

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0437 AC: 6659 AN: 152218 Hom.: 198 Cov.: 33 AF XY: 0.0434 AC XY: 3232 AN XY: 74422

Gnomad4 AFR AF: 0.00994

Gnomad4 AMR AF: 0.0406

Gnomad4 ASJ AF: 0.0476

Gnomad4 EAS AF: 0.0334

Gnomad4 SAS AF: 0.0293

Gnomad4 FIN AF: 0.0798

Gnomad4 NFE AF: 0.0617

Gnomad4 OTH AF: 0.0345

Alfa AF: 0.0562 Hom.: 340

Bravo AF: 0.0402

Asia WGS AF: 0.0330 AC: 115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.24
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4657270; hg19: chr1-163378647;