rs7984869

Positions:

• chr13-86116392-G-T

Variant summary

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

The ENST00000445967.1(ENSG00000232252):​n.148+43466G>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 0.592 in 151,842 control chromosomes in the GnomAD database, including 27,126 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 (27126 hom., cov: 31)
• Consequence: ENST00000445967.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 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
	ENST00000445967.1	n.148+43466G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89737 AN: 151724 Hom.: 27092 Cov.: 31

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.592 AC: 89819 AN: 151842 Hom.: 27126 Cov.: 31 AF XY: 0.591 AC XY: 43850 AN XY: 74210

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.553

Alfa AF: 0.549 Hom.: 38753

Bravo AF: 0.589

Asia WGS AF: 0.455 AC: 1583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.9
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7984869; hg19: chr13-86690527;