rs772492

Variant names:

• chr4-89451415-T-C
• rs772492
• ENST00000659878.1:n.359+40097T>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 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: ENSG00000251095 ENST00000659878.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

Genes affected

ENSG00000251095 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251095	ENST00000659878.1	n.359+40097T>C		intron_variant	Intron 1 of 2

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;