rs4656849

Variant names:

• chr1-159753731-A-G
• rs4656849

Your query was ambiguous. Multiple possible variants found:

• chr1-159753731-A-G
• chr1-159753731-A-T

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 0.71 in 152,034 control chromosomes in the GnomAD database, including 39,099 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 0.71 (39099 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

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 (EAS) allele frequency at 95% confidence interval = 0.83 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: 0.710 AC: 107901 AN: 151916 Hom.: 39047 Cov.: 31

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.710 AC: 108010 AN: 152034 Hom.: 39099 Cov.: 31 AF XY: 0.713 AC XY: 52977 AN XY: 74318

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.713

Alfa AF: 0.638 Hom.: 62324

Bravo AF: 0.724

Asia WGS AF: 0.741 AC: 2578 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	6.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4656849; hg19: chr1-159723521;