rs924033

Positions:

• chr4-89514402-T-G

Variant summary

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

The ENST00000659878.1(ENSG00000251095):​n.360-73419T>G 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 0.0539 in 152,220 control chromosomes in the GnomAD database, including 305 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 0.054 (305 hom., cov: 31)
• Consequence: ENST00000659878.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659878.1	n.360-73419T>G		intron_variant, non_coding_transcript_variant
	ENST00000659714.1	n.546+22908T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0540 AC: 8214 AN: 152102 Hom.: 305 Cov.: 31

Gnomad AFR AF: 0.0146

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.0257

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00601

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0539 AC: 8212 AN: 152220 Hom.: 305 Cov.: 31 AF XY: 0.0525 AC XY: 3910 AN XY: 74422

Gnomad4 AFR AF: 0.0145

Gnomad4 AMR AF: 0.0319

Gnomad4 ASJ AF: 0.0257

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00602

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0846

Gnomad4 OTH AF: 0.0398

Alfa AF: 0.0728 Hom.: 259

Bravo AF: 0.0474

Asia WGS AF: 0.00751 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs924033; hg19: chr4-90435553;