rs9296102

chr6-33902029-G-Achr6-33902029-G-T

Variant summary

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

The ENST00000451317.2(ENSG00000233183):n.119+1556G>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 0.407 in 151,996 control chromosomes in the GnomAD database, including 13,329 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 0.41 (13329 hom., cov: 32)
• Consequence: ENST00000451317.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375026	XR_926712.4	n.5014+3887G>A		intron_variant, non_coding_transcript_variant
LOC105375026	XR_926713.4	n.262+8639G>A		intron_variant, non_coding_transcript_variant
LOC105375026	XR_926718.3	n.927+5542G>A		intron_variant, non_coding_transcript_variant
LOC105375026	XR_926719.3	n.110+8791G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000451317.2	n.119+1556G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61820 AN: 151878 Hom.: 13300 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.407 AC: 61898 AN: 151996 Hom.: 13329 Cov.: 32 AF XY: 0.405 AC XY: 30116 AN XY: 74306

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.409

Alfa AF: 0.351 Hom.: 10154

Bravo AF: 0.416

Asia WGS AF: 0.446 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	7.1
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9296102; hg19: chr6-33869806;