rs1415639

Positions:

• chr13-44705575-G-A

Variant summary

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

The ENST00000611081.1(ENSG00000276527):​n.93+9726C>T 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 0.122 in 152,058 control chromosomes in the GnomAD database, including 2,174 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 0.12 (2174 hom., cov: 32)
• Consequence: ENST00000611081.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370185	XR_941929.4	n.379+10120C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000611081.1	n.93+9726C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18527 AN: 151940 Hom.: 2167 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0635

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.0494

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.0451

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0453

Gnomad OTH AF: 0.0950

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

GnomAD4 genome AF: 0.122 AC: 18566 AN: 152058 Hom.: 2174 Cov.: 32 AF XY: 0.119 AC XY: 8850 AN XY: 74370

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.0635

Gnomad4 ASJ AF: 0.0585

Gnomad4 EAS AF: 0.0493

Gnomad4 SAS AF: 0.0926

Gnomad4 FIN AF: 0.0451

Gnomad4 NFE AF: 0.0453

Gnomad4 OTH AF: 0.0940

Alfa AF: 0.0981 Hom.: 370

Bravo AF: 0.131

Asia WGS AF: 0.101 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.51
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1415639; hg19: chr13-45279711;