chr9-134520718-C-T

Variant names:

• chr9-134520718-C-T
• rs1536480
• ENST00000444936.3:n.313+98C>T

Variant summary

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

The ENST00000444936.3(ENSG00000228877):​n.313+98C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,008 control chromosomes in the GnomAD database, including 10,736 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 0.37 (10735 hom., cov: 32)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: ENSG00000228877 ENST00000444936.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 3 publications found

Genes affected

ENSG00000228877 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444936.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC100506532	NR_188441.1		n.183+15172C>T		intron	N/A
	LOC100506532	NR_188442.1		n.612+98C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228877	ENST00000444936.3	TSL:2	n.313+98C>T		intron	N/A
	ENSG00000228877	ENST00000745249.1		n.1011+15172C>T		intron	N/A
	ENSG00000228877	ENST00000745250.1		n.270+15172C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56216 AN: 151884 Hom.: 10739 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.393

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 AF XY: 0.667 AC XY: 4 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.370 AC: 56240 AN: 152002 Hom.: 10735 Cov.: 32 AF XY: 0.368 AC XY: 27341 AN XY: 74292

African (AFR) AF: 0.296 AC: 12274 AN: 41438

American (AMR) AF: 0.436 AC: 6662 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1587 AN: 3466

East Asian (EAS) AF: 0.436 AC: 2252 AN: 5160

South Asian (SAS) AF: 0.323 AC: 1552 AN: 4806

European-Finnish (FIN) AF: 0.326 AC: 3436 AN: 10556

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.398 AC: 27069 AN: 67970

Other (OTH) AF: 0.391 AC: 825 AN: 2110

Alfa AF: 0.380 Hom.: 1441

Bravo AF: 0.380

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.67
DANN	Benign	0.23
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1536480; hg19: chr9-137412564;