chr1-160361229-A-G

Variant names:

• chr1-160361229-A-G
• rs4656256

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 0.378 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
• Publications: 12 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 (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

African (AFR) AF: 0.765 AC: 31699 AN: 41438

American (AMR) AF: 0.251 AC: 3841 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3468

East Asian (EAS) AF: 0.357 AC: 1843 AN: 5168

South Asian (SAS) AF: 0.422 AC: 2028 AN: 4806

European-Finnish (FIN) AF: 0.243 AC: 2562 AN: 10556

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14066 AN: 67990

Other (OTH) AF: 0.339 AC: 717 AN: 2112

Alfa AF: 0.256 Hom.: 11339

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
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4656256; hg19: chr1-160331019;