rs876347

Variant names:

• chr9-118268751-A-G
• rs876347
• ENST00000697639.1:n.1576-37438A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-118268751-A-G
• chr9-118268751-A-T

Variant summary

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

The ENST00000697639.1(ENSG00000284977):​n.1576-37438A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,886 control chromosomes in the GnomAD database, including 3,235 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 0.19 (3235 hom., cov: 31)
• Consequence: ENSG00000284977 ENST00000697639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829
• Publications: 10 publications found

Genes affected

ENSG00000284977 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.266 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
ENSG00000284977	ENST00000697639.1	n.1576-37438A>G		intron_variant	Intron 12 of 12

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28508 AN: 151766 Hom.: 3234 Cov.: 31

Gnomad AFR AF: 0.0483

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.188 AC: 28510 AN: 151886 Hom.: 3235 Cov.: 31 AF XY: 0.189 AC XY: 13996 AN XY: 74218

African (AFR) AF: 0.0482 AC: 2000 AN: 41534

American (AMR) AF: 0.273 AC: 4161 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 563 AN: 3462

East Asian (EAS) AF: 0.191 AC: 977 AN: 5102

South Asian (SAS) AF: 0.225 AC: 1085 AN: 4818

European-Finnish (FIN) AF: 0.246 AC: 2606 AN: 10578

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16318 AN: 67850

Other (OTH) AF: 0.195 AC: 412 AN: 2108

Alfa AF: 0.221 Hom.: 10222

Bravo AF: 0.188

Asia WGS AF: 0.211 AC: 731 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.14
DANN	Benign	0.73
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs876347; hg19: chr9-121031029;