rs1967017

Variant names:

• chr1-145711421-A-G
• rs1967017

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 0.429 in 152,054 control chromosomes in the GnomAD database, including 15,104 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 0.43 (15104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.652
• Publications: 50 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 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: 0.429 AC: 65224 AN: 151936 Hom.: 15103 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.429 AC: 65257 AN: 152054 Hom.: 15104 Cov.: 32 AF XY: 0.428 AC XY: 31796 AN XY: 74322

African (AFR) AF: 0.293 AC: 12157 AN: 41476

American (AMR) AF: 0.419 AC: 6396 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1385 AN: 3470

East Asian (EAS) AF: 0.162 AC: 839 AN: 5178

South Asian (SAS) AF: 0.319 AC: 1538 AN: 4822

European-Finnish (FIN) AF: 0.533 AC: 5633 AN: 10566

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35802 AN: 67958

Other (OTH) AF: 0.415 AC: 875 AN: 2106

Alfa AF: 0.486 Hom.: 37143

Bravo AF: 0.413

Asia WGS AF: 0.229 AC: 796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	16
DANN	Benign	0.79
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs1967017; hg19: chr1-145723645;