chr9-31678814-C-T

Variant names:

• chr9-31678814-C-T
• rs990708
• ENST00000804476.1:n.111-44568G>A

Variant summary

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

The ENST00000804476.1(ENSG00000304547):​n.111-44568G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 151,662 control chromosomes in the GnomAD database, including 4,428 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 0.24 (4428 hom., cov: 32)
• Consequence: ENSG00000304547 ENST00000804476.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 2 publications found

Genes affected

ENSG00000304547 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.292 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
ENSG00000304547	ENST00000804476.1	n.111-44568G>A		intron_variant	Intron 1 of 2
ENSG00000304547	ENST00000804477.1	n.139+14423G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36568 AN: 151544 Hom.: 4428 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.241 AC: 36588 AN: 151662 Hom.: 4428 Cov.: 32 AF XY: 0.242 AC XY: 17897 AN XY: 74062

African (AFR) AF: 0.229 AC: 9493 AN: 41400

American (AMR) AF: 0.232 AC: 3521 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 743 AN: 3460

East Asian (EAS) AF: 0.242 AC: 1241 AN: 5132

South Asian (SAS) AF: 0.304 AC: 1470 AN: 4828

European-Finnish (FIN) AF: 0.249 AC: 2627 AN: 10558

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16677 AN: 67766

Other (OTH) AF: 0.209 AC: 441 AN: 2110

Alfa AF: 0.240 Hom.: 3127

Bravo AF: 0.234

Asia WGS AF: 0.268 AC: 932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.52
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs990708; hg19: chr9-31678812;