chr1-30587017-A-C

Variant names:

• chr1-30587017-A-C
• rs555920

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 0.284 in 152,040 control chromosomes in the GnomAD database, including 7,101 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 0.28 (7101 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.455 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: 0.283 AC: 43035 AN: 151920 Hom.: 7077 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.284 AC: 43104 AN: 152040 Hom.: 7101 Cov.: 32 AF XY: 0.281 AC XY: 20896 AN XY: 74330

African (AFR) AF: 0.460 AC: 19075 AN: 41456

American (AMR) AF: 0.201 AC: 3066 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 800 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1746 AN: 5164

South Asian (SAS) AF: 0.124 AC: 597 AN: 4816

European-Finnish (FIN) AF: 0.271 AC: 2868 AN: 10586

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14121 AN: 67964

Other (OTH) AF: 0.241 AC: 507 AN: 2104

Alfa AF: 0.208 Hom.: 1456

Bravo AF: 0.289

Asia WGS AF: 0.247 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.85
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs555920; hg19: chr1-31059864; COSMIC: COSV59935839;