1-114294615-A-G

Variant names:

• chr1-114294615-A-G
• rs10489666

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 0.884 in 152,230 control chromosomes in the GnomAD database, including 59,676 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 0.88 (59676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.884 AC: 134442 AN: 152112 Hom.: 59614 Cov.: 32

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.884 AC: 134565 AN: 152230 Hom.: 59676 Cov.: 32 AF XY: 0.887 AC XY: 66052 AN XY: 74428

African (AFR) AF: 0.825 AC: 34231 AN: 41508

American (AMR) AF: 0.897 AC: 13706 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2855 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5183 AN: 5184

South Asian (SAS) AF: 0.964 AC: 4658 AN: 4830

European-Finnish (FIN) AF: 0.924 AC: 9804 AN: 10608

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61136 AN: 68022

Other (OTH) AF: 0.879 AC: 1858 AN: 2114

Alfa AF: 0.896 Hom.: 16970

Bravo AF: 0.877

Asia WGS AF: 0.970 AC: 3372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.21
DANN	Benign	0.41
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10489666; hg19: chr1-114837237;