rs4658504

Variant names:

• chr1-242877745-T-C
• rs4658504

Your query was ambiguous. Multiple possible variants found:

• chr1-242877745-T-C
• chr1-242877745-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.855 AC: 35459 AN: 41480

American (AMR) AF: 0.699 AC: 10669 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1838 AN: 3468

East Asian (EAS) AF: 0.874 AC: 4520 AN: 5174

South Asian (SAS) AF: 0.864 AC: 4164 AN: 4818

European-Finnish (FIN) AF: 0.529 AC: 5574 AN: 10540

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42663 AN: 67974

Other (OTH) AF: 0.681 AC: 1439 AN: 2112

Alfa AF: 0.649 Hom.: 58040

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
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs4658504; hg19: chr1-243041047;