chr1-11899159-G-A

Variant names:

• chr1-11899159-G-A
• rs1999594

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 0.519 in 152,060 control chromosomes in the GnomAD database, including 21,118 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 (21118 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.636 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: 0.519 AC: 78793 AN: 151942 Hom.: 21072 Cov.: 33

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.519 AC: 78905 AN: 152060 Hom.: 21118 Cov.: 33 AF XY: 0.525 AC XY: 39002 AN XY: 74318

African (AFR) AF: 0.609 AC: 25281 AN: 41484

American (AMR) AF: 0.431 AC: 6581 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1191 AN: 3466

East Asian (EAS) AF: 0.621 AC: 3207 AN: 5168

South Asian (SAS) AF: 0.655 AC: 3157 AN: 4820

European-Finnish (FIN) AF: 0.604 AC: 6379 AN: 10570

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31635 AN: 67948

Other (OTH) AF: 0.499 AC: 1056 AN: 2116

Alfa AF: 0.478 Hom.: 77613

Bravo AF: 0.504

Asia WGS AF: 0.669 AC: 2328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	7.3
DANN	Benign	0.78
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1999594; hg19: chr1-11959216;