13-21661445-A-G

Position:

• chr13-21661445-A-G

Variant summary

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

The ENST00000701135.1(ENSG00000289860):​n.277+9152T>C 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 0.59 in 151,948 control chromosomes in the GnomAD database, including 26,882 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 0.59 (26882 hom., cov: 31)
• Consequence: ENST00000701135.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000701135.1	n.277+9152T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89604 AN: 151830 Hom.: 26839 Cov.: 31

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.590 AC: 89695 AN: 151948 Hom.: 26882 Cov.: 31 AF XY: 0.581 AC XY: 43185 AN XY: 74278

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.559

Alfa AF: 0.563 Hom.: 11050

Bravo AF: 0.586

Asia WGS AF: 0.555 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs829209; hg19: chr13-22235584;