rs919679

Variant names:

• chr1-166287925-C-T
• rs919679
• ENST00000653824.3:n.221-47403C>T

Variant summary

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

The ENST00000653824.3(ENSG00000229588):​n.221-47403C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 151,970 control chromosomes in the GnomAD database, including 31,891 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 0.62 (31891 hom., cov: 31)
• Consequence: ENSG00000229588 ENST00000653824.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547
• Publications: 1 publications found

Genes affected

ENSG00000229588 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268276	XR_002958633.2	n.179-47403C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229588	ENST00000653824.3	n.221-47403C>T		intron_variant	Intron 1 of 2
ENSG00000229588	ENST00000829274.1	n.179-50975C>T		intron_variant	Intron 1 of 1
ENSG00000229588	ENST00000829275.1	n.190-47403C>T		intron_variant	Intron 1 of 1
ENSG00000229588	ENST00000829276.1	n.141-47403C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93522 AN: 151852 Hom.: 31890 Cov.: 31

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.616 AC: 93541 AN: 151970 Hom.: 31891 Cov.: 31 AF XY: 0.615 AC XY: 45675 AN XY: 74302

African (AFR) AF: 0.307 AC: 12709 AN: 41398

American (AMR) AF: 0.602 AC: 9184 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2260 AN: 3466

East Asian (EAS) AF: 0.544 AC: 2808 AN: 5164

South Asian (SAS) AF: 0.619 AC: 2980 AN: 4818

European-Finnish (FIN) AF: 0.779 AC: 8221 AN: 10560

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.781 AC: 53098 AN: 67976

Other (OTH) AF: 0.607 AC: 1285 AN: 2116

Alfa AF: 0.707 Hom.: 13855

Bravo AF: 0.592

Asia WGS AF: 0.557 AC: 1941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.77
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs919679; hg19: chr1-166257162;