9-38737020-T-C

Variant names:

• chr9-38737020-T-C
• rs4559327
• ENST00000835853.1:n.185+9228T>C

Variant summary

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

The ENST00000835853.1(ENSG00000308694):​n.185+9228T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,128 control chromosomes in the GnomAD database, including 7,837 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 0.32 (7837 hom., cov: 33)
• Consequence: ENSG00000308694 ENST00000835853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 1 publications found

Genes affected

ENSG00000308694 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.355 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
ENSG00000308694	ENST00000835853.1	n.185+9228T>C		intron_variant	Intron 1 of 1
ENSG00000308694	ENST00000835854.1	n.278-1090T>C		intron_variant	Intron 2 of 4
ENSG00000308694	ENST00000835855.1	n.72+9228T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48425 AN: 152010 Hom.: 7820 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.319 AC: 48490 AN: 152128 Hom.: 7837 Cov.: 33 AF XY: 0.321 AC XY: 23878 AN XY: 74360

African (AFR) AF: 0.354 AC: 14701 AN: 41500

American (AMR) AF: 0.363 AC: 5539 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1035 AN: 3472

East Asian (EAS) AF: 0.288 AC: 1488 AN: 5170

South Asian (SAS) AF: 0.307 AC: 1478 AN: 4816

European-Finnish (FIN) AF: 0.305 AC: 3232 AN: 10586

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19888 AN: 67990

Other (OTH) AF: 0.330 AC: 698 AN: 2112

Alfa AF: 0.290 Hom.: 1029

Bravo AF: 0.324

Asia WGS AF: 0.269 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.72
DANN	Benign	0.37
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4559327; hg19: chr9-38737017;