rs9942773

Variant names:

• chr8-114108798-A-C
• rs9942773
• ENST00000759927.1:n.45+4842T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-114108798-A-C
• chr8-114108798-A-T

Variant summary

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

The ENST00000759927.1(ENSG00000299025):​n.45+4842T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 151,848 control chromosomes in the GnomAD database, including 4,925 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 0.25 (4925 hom., cov: 31)
• Consequence: ENSG00000299025 ENST00000759927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587
• Publications: 5 publications found

Genes affected

ENSG00000299025 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000759927.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299025	ENST00000759927.1		n.45+4842T>G		intron	N/A
	ENSG00000299025	ENST00000759928.1		n.139+4076T>G		intron	N/A
	ENSG00000299025	ENST00000759929.1		n.139+4076T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37534 AN: 151730 Hom.: 4919 Cov.: 31

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0425

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.247 AC: 37560 AN: 151848 Hom.: 4925 Cov.: 31 AF XY: 0.241 AC XY: 17908 AN XY: 74172

African (AFR) AF: 0.303 AC: 12558 AN: 41396

American (AMR) AF: 0.170 AC: 2603 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3470

East Asian (EAS) AF: 0.0428 AC: 219 AN: 5122

South Asian (SAS) AF: 0.134 AC: 643 AN: 4810

European-Finnish (FIN) AF: 0.229 AC: 2418 AN: 10554

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.258 AC: 17494 AN: 67924

Other (OTH) AF: 0.226 AC: 474 AN: 2100

Alfa AF: 0.248 Hom.: 7947

Bravo AF: 0.246

Asia WGS AF: 0.116 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.42
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs9942773; hg19: chr8-115121027;