9-73182919-G-A

Variant names:

• chr9-73182919-G-A
• rs4256646
• ENST00000715863.1:n.262+40531C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000715863.1(ENSG00000293607):​n.262+40531C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,972 control chromosomes in the GnomAD database, including 19,089 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 0.50 (19089 hom., cov: 33)
• Consequence: ENSG00000293607 ENST00000715863.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 6 publications found

Genes affected

ENSG00000293607 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.545 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
ENSG00000293607	ENST00000715863.1	n.262+40531C>T		intron_variant	Intron 2 of 3
ENSG00000293607	ENST00000715864.1	n.310-478C>T		intron_variant	Intron 3 of 3
ENSG00000293607	ENST00000715865.1	n.277-478C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76046 AN: 151854 Hom.: 19093 Cov.: 33

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.500 AC: 76060 AN: 151972 Hom.: 19089 Cov.: 33 AF XY: 0.500 AC XY: 37132 AN XY: 74274

African (AFR) AF: 0.468 AC: 19383 AN: 41440

American (AMR) AF: 0.498 AC: 7610 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1747 AN: 3470

East Asian (EAS) AF: 0.465 AC: 2405 AN: 5174

South Asian (SAS) AF: 0.562 AC: 2711 AN: 4822

European-Finnish (FIN) AF: 0.488 AC: 5142 AN: 10544

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35377 AN: 67944

Other (OTH) AF: 0.516 AC: 1090 AN: 2112

Alfa AF: 0.513 Hom.: 34429

Bravo AF: 0.496

Asia WGS AF: 0.492 AC: 1704 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.64
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs4256646; hg19: chr9-75797835;