chr1-186611692-G-T

Variant names:

• chr1-186611692-G-T
• rs11584662

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 0.502 in 151,936 control chromosomes in the GnomAD database, including 19,504 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 0.50 (19504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 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: 0.502 AC: 76150 AN: 151818 Hom.: 19453 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.502 AC: 76258 AN: 151936 Hom.: 19504 Cov.: 32 AF XY: 0.501 AC XY: 37218 AN XY: 74272

African (AFR) AF: 0.587 AC: 24305 AN: 41438

American (AMR) AF: 0.465 AC: 7102 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1490 AN: 3468

East Asian (EAS) AF: 0.600 AC: 3097 AN: 5160

South Asian (SAS) AF: 0.474 AC: 2280 AN: 4814

European-Finnish (FIN) AF: 0.461 AC: 4861 AN: 10548

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31612 AN: 67934

Other (OTH) AF: 0.474 AC: 999 AN: 2108

Alfa AF: 0.449 Hom.: 8125

Bravo AF: 0.509

Asia WGS AF: 0.561 AC: 1950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.16
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs11584662; hg19: chr1-186580824;