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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000669705.1. 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
	ENSG00000286780	ENST00000669705.1		n.69+5209T>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1477921;

hg19: chr13-107018153;