rs142331957

Variant names:

• chr9-11669879-G-C
• rs142331957
• ENST00000649122.1:n.204+29045G>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000649122.1(ENSG00000285784):​n.204+29045G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00555 in 151,450 control chromosomes in the GnomAD database, including 13 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 0.0056 (13 hom., cov: 32)
• Consequence: ENSG00000285784 ENST00000649122.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 0 publications found

Genes affected

ENSG00000285784 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS2: High Homozygotes in GnomAd4 at 13 gene

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
ENSG00000285784	ENST00000649122.1	n.204+29045G>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.00557 AC: 843 AN: 151334 Hom.: 13 Cov.: 32

Gnomad AFR AF: 0.0115

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00497

Gnomad ASJ AF: 0.0462

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00170

Gnomad OTH AF: 0.00818

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

GnomAD4 genome AF: 0.00555 AC: 841 AN: 151450 Hom.: 13 Cov.: 32 AF XY: 0.00542 AC XY: 401 AN XY: 74000

African (AFR) AF: 0.0114 AC: 473 AN: 41386

American (AMR) AF: 0.00497 AC: 75 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.0462 AC: 160 AN: 3462

East Asian (EAS) AF: 0.00 AC: 0 AN: 5124

South Asian (SAS) AF: 0.00 AC: 0 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10530

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.00170 AC: 115 AN: 67718

Other (OTH) AF: 0.00810 AC: 17 AN: 2100

Alfa AF: 0.00534 Hom.: 0

Bravo AF: 0.00650

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.93
DANN	Benign	0.17
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs142331957; hg19: chr9-11669879;