rs1477921

Variant names:

• chr13-106365805-A-C
• rs1477921
• ENST00000669705.1:n.69+5209T>G

Your query was ambiguous. Multiple possible variants found:

• chr13-106365805-A-C
• chr13-106365805-A-G

Variant summary

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

The ENST00000669705.1(ENSG00000286780):​n.69+5209T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,968 control chromosomes in the GnomAD database, including 18,808 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 0.45 (18808 hom., cov: 31)
• Consequence: ENSG00000286780 ENST00000669705.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 1 publications found

Genes affected

ENSG00000286780 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984626	XR_001750000.2	n.186+7994T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286780	ENST00000669705.1	n.69+5209T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68019 AN: 151850 Hom.: 18801 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.448 AC: 68026 AN: 151968 Hom.: 18808 Cov.: 31 AF XY: 0.455 AC XY: 33786 AN XY: 74292

African (AFR) AF: 0.109 AC: 4535 AN: 41500

American (AMR) AF: 0.582 AC: 8875 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1732 AN: 3472

East Asian (EAS) AF: 0.528 AC: 2720 AN: 5156

South Asian (SAS) AF: 0.423 AC: 2037 AN: 4818

European-Finnish (FIN) AF: 0.616 AC: 6500 AN: 10546

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40119 AN: 67910

Other (OTH) AF: 0.445 AC: 939 AN: 2110

Alfa AF: 0.545 Hom.: 11998

Bravo AF: 0.430

Asia WGS AF: 0.459 AC: 1591 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.81
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1477921; hg19: chr13-107018153;