1-19845367-G-A

Variant names:

• chr1-19845367-G-A
• rs6426833

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 0.522 in 152,114 control chromosomes in the GnomAD database, including 21,086 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 0.52 (21086 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 69 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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: 0.522 AC: 79384 AN: 151994 Hom.: 21087 Cov.: 34

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.522 AC: 79409 AN: 152114 Hom.: 21086 Cov.: 34 AF XY: 0.523 AC XY: 38904 AN XY: 74354

African (AFR) AF: 0.462 AC: 19150 AN: 41488

American (AMR) AF: 0.507 AC: 7742 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1993 AN: 3464

East Asian (EAS) AF: 0.745 AC: 3857 AN: 5178

South Asian (SAS) AF: 0.675 AC: 3256 AN: 4822

European-Finnish (FIN) AF: 0.487 AC: 5145 AN: 10562

Middle Eastern (MID) AF: 0.695 AC: 203 AN: 292

European-Non Finnish (NFE) AF: 0.534 AC: 36351 AN: 68010

Other (OTH) AF: 0.539 AC: 1139 AN: 2114

Alfa AF: 0.539 Hom.: 101479

Bravo AF: 0.516

Asia WGS AF: 0.699 AC: 2429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.8
DANN	Benign	0.70
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs6426833; hg19: chr1-20171860;