1-214265985-A-C

Variant names:

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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722830.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294336	ENST00000722830.1		n.205+12729T>G		intron	N/A
	ENSG00000294336	ENST00000722832.1		n.313-3021T>G		intron	N/A
	ENSG00000294336	ENST00000722833.1		n.262-1010T>G		intron	N/A

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 v4.9

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;