rs1477921

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000669705.1(ENSG00000286780):​n.69+5209T>G variant causes a intron, non coding transcript 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: ENST00000669705.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107984626	XR_001750000.2	n.186+7994T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000669705.1	n.69+5209T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.445

Alfa AF: 0.542 Hom.: 10725

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1477921; hg19: chr13-107018153;