rs766499

Variant names:

• chr1-214265985-A-C
• rs766499
• ENST00000722830.1:n.205+12729T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-214265985-A-C
• chr1-214265985-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000722830.1(ENSG00000294336):​n.205+12729T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.931 in 152,294 control chromosomes in the GnomAD database, including 66,345 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 0.93 (66345 hom., cov: 33)
• Consequence: ENSG00000294336 ENST00000722830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 4 publications found

Genes affected

ENSG00000294336 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904509	XR_007066876.1	n.2324-3021T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294336	ENST00000722830.1	n.205+12729T>G		intron_variant	Intron 1 of 2
ENSG00000294336	ENST00000722832.1	n.313-3021T>G		intron_variant	Intron 1 of 1
ENSG00000294336	ENST00000722833.1	n.262-1010T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.931 AC: 141617 AN: 152176 Hom.: 66291 Cov.: 33

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.931 AC: 141727 AN: 152294 Hom.: 66345 Cov.: 33 AF XY: 0.926 AC XY: 68957 AN XY: 74464

African (AFR) AF: 0.987 AC: 41006 AN: 41562

American (AMR) AF: 0.828 AC: 12665 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2951 AN: 3472

East Asian (EAS) AF: 0.691 AC: 3574 AN: 5174

South Asian (SAS) AF: 0.872 AC: 4207 AN: 4826

European-Finnish (FIN) AF: 0.961 AC: 10197 AN: 10610

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.942 AC: 64079 AN: 68040

Other (OTH) AF: 0.907 AC: 1918 AN: 2114

Alfa AF: 0.929 Hom.: 27806

Bravo AF: 0.921

Asia WGS AF: 0.807 AC: 2808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.64
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs766499; hg19: chr1-214439328;