rs772492

chr4-89451415-T-C

Variant summary

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

The ENST00000659878.1(ENSG00000251095):n.359+40097T>C 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 0.73 in 152,060 control chromosomes in the GnomAD database, including 40,783 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 0.73 (40783 hom., cov: 31)
• Consequence: ENST00000659878.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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.359+40097T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110829 AN: 151942 Hom.: 40742 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.730 AC: 110928 AN: 152060 Hom.: 40783 Cov.: 31 AF XY: 0.737 AC XY: 54754 AN XY: 74326

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.877

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.747

Alfa AF: 0.703 Hom.: 78124

Bravo AF: 0.727

Asia WGS AF: 0.918 AC: 3189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.2
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs772492; hg19: chr4-90372566;