1-86546111-C-T

Variant names:

• chr1-86546111-C-T
• rs11807298

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 0.138 in 152,014 control chromosomes in the GnomAD database, including 1,798 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 0.14 (1798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 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: 0.138 AC: 20960 AN: 151896 Hom.: 1793 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.0613

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.138 AC: 20986 AN: 152014 Hom.: 1798 Cov.: 32 AF XY: 0.134 AC XY: 9922 AN XY: 74314

African (AFR) AF: 0.241 AC: 9965 AN: 41428

American (AMR) AF: 0.102 AC: 1563 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 416 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5182

South Asian (SAS) AF: 0.0878 AC: 423 AN: 4816

European-Finnish (FIN) AF: 0.0613 AC: 647 AN: 10552

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7579 AN: 67970

Other (OTH) AF: 0.129 AC: 273 AN: 2112

Alfa AF: 0.126 Hom.: 184

Bravo AF: 0.144

Asia WGS AF: 0.0490 AC: 171 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	1.0
DANN	Benign	0.43
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs11807298; hg19: chr1-87011794;