rs4658535

Positions:

• chr1-241895919-G-A
• chr1-241895919-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 0.241 in 151,962 control chromosomes in the GnomAD database, including 5,066 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 0.24 (5066 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 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: 0.241 AC: 36583 AN: 151842 Hom.: 5061 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.241 AC: 36635 AN: 151962 Hom.: 5066 Cov.: 32 AF XY: 0.246 AC XY: 18296 AN XY: 74284

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.245

Alfa AF: 0.198 Hom.: 6568

Bravo AF: 0.262

Asia WGS AF: 0.392 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4658535; hg19: chr1-242059221;