rs4285692

Variant names:

• chr1-159744359-T-C
• rs4285692

Your query was ambiguous. Multiple possible variants found:

• chr1-159744359-T-C
• chr1-159744359-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 0.629 in 152,058 control chromosomes in the GnomAD database, including 31,065 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 0.63 (31065 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 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: 0.628 AC: 95460 AN: 151940 Hom.: 31002 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.629 AC: 95588 AN: 152058 Hom.: 31065 Cov.: 32 AF XY: 0.630 AC XY: 46851 AN XY: 74332

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.613

Alfa AF: 0.544 Hom.: 37098

Bravo AF: 0.647

Asia WGS AF: 0.642 AC: 2236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.52
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4285692; hg19: chr1-159714149;