rs4656849

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;