chr1-217888069-C-T

Variant names:

• chr1-217888069-C-T
• rs7530786
• ENST00000848869.1:n.993+28544G>A

Variant summary

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

The ENST00000848869.1(ENSG00000286775):​n.993+28544G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0969 in 152,226 control chromosomes in the GnomAD database, including 786 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 0.097 (786 hom., cov: 32)
• Consequence: ENSG00000286775 ENST00000848869.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 3 publications found

Genes affected

ENSG00000286775 (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 = 0.141 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848869.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286775	ENST00000848869.1		n.993+28544G>A		intron	N/A
	ENSG00000310360	ENST00000849288.1		n.-66G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0969 AC: 14737 AN: 152108 Hom.: 785 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0715

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.0626

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0647

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0820

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0969 AC: 14753 AN: 152226 Hom.: 786 Cov.: 32 AF XY: 0.0961 AC XY: 7149 AN XY: 74424

African (AFR) AF: 0.144 AC: 5974 AN: 41526

American (AMR) AF: 0.0713 AC: 1090 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0839 AC: 291 AN: 3470

East Asian (EAS) AF: 0.0631 AC: 326 AN: 5166

South Asian (SAS) AF: 0.100 AC: 483 AN: 4824

European-Finnish (FIN) AF: 0.0647 AC: 687 AN: 10620

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0820 AC: 5576 AN: 68014

Other (OTH) AF: 0.0998 AC: 211 AN: 2114

Alfa AF: 0.0854 Hom.: 344

Bravo AF: 0.0979

Asia WGS AF: 0.0640 AC: 222 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	1.2
DANN	Benign	0.36
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs7530786; hg19: chr1-218061411;