rs4656256

Variant names:

• chr1-160361229-A-G
• rs4656256

Your query was ambiguous. Multiple possible variants found:

• chr1-160361229-A-G
• chr1-160361229-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 0.378 in 152,030 control chromosomes in the GnomAD database, including 15,433 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 0.38 (15433 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

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 (AFR) allele frequency at 95% confidence interval = 0.758 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: 0.378 AC: 57420 AN: 151914 Hom.: 15376 Cov.: 32

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.378 AC: 57537 AN: 152030 Hom.: 15433 Cov.: 32 AF XY: 0.377 AC XY: 27997 AN XY: 74292

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.339

Alfa AF: 0.242 Hom.: 7646

Bravo AF: 0.391

Asia WGS AF: 0.434 AC: 1505 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	0.83
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4656256; hg19: chr1-160331019;