rs4733142

chr8-33017609-T-Achr8-33017609-T-Cchr8-33017609-T-G

Variant summary

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

The ENST00000659524.1(ENSG00000247134):n.182-24026T>A 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 0.418 in 151,926 control chromosomes in the GnomAD database, including 14,781 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 0.42 (14781 hom., cov: 32)
• Consequence: ENST00000659524.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972

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 (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379362	XR_949653.4	n.233+21293T>A		intron_variant, non_coding_transcript_variant
LOC105379362	XR_949654.4	n.352+21293T>A		intron_variant, non_coding_transcript_variant
LOC105379362	XR_949656.4	n.118-24026T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659524.1	n.182-24026T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63384 AN: 151808 Hom.: 14762 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.418 AC: 63442 AN: 151926 Hom.: 14781 Cov.: 32 AF XY: 0.423 AC XY: 31407 AN XY: 74254

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.972

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.463

Alfa AF: 0.403 Hom.: 1627

Bravo AF: 0.433

Asia WGS AF: 0.760 AC: 2638 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.6
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4733142; hg19: chr8-32875127;