rs4658504

Positions:

• chr1-242877745-T-C
• chr1-242877745-T-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 0.704 in 152,040 control chromosomes in the GnomAD database, including 38,742 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 0.70 (38742 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

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 (EAS) allele frequency at 95% confidence interval = 0.852 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: 0.704 AC: 106956 AN: 151922 Hom.: 38696 Cov.: 31

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.704 AC: 107065 AN: 152040 Hom.: 38742 Cov.: 31 AF XY: 0.704 AC XY: 52327 AN XY: 74298

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.681

Alfa AF: 0.639 Hom.: 40159

Bravo AF: 0.716

Asia WGS AF: 0.872 AC: 3032 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	2.7
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4658504; hg19: chr1-243041047;