9-118516013-G-A

Variant names:

• chr9-118516013-G-A
• rs4132476
• ENST00000770012.1:n.344-1055C>T

Variant summary

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

The ENST00000770012.1(ENSG00000300201):​n.344-1055C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,044 control chromosomes in the GnomAD database, including 1,711 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 0.14 (1711 hom., cov: 32)
• Consequence: ENSG00000300201 ENST00000770012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 4 publications found

Genes affected

ENSG00000300201 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770012.1. 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
	ENSG00000300201	ENST00000770012.1		n.344-1055C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21762 AN: 151924 Hom.: 1703 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.00483

Gnomad SAS AF: 0.0717

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.143 AC: 21784 AN: 152044 Hom.: 1711 Cov.: 32 AF XY: 0.141 AC XY: 10461 AN XY: 74344

African (AFR) AF: 0.213 AC: 8828 AN: 41422

American (AMR) AF: 0.120 AC: 1837 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3468

East Asian (EAS) AF: 0.00484 AC: 25 AN: 5168

South Asian (SAS) AF: 0.0713 AC: 344 AN: 4822

European-Finnish (FIN) AF: 0.109 AC: 1156 AN: 10588

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8793 AN: 67988

Other (OTH) AF: 0.145 AC: 306 AN: 2108

Alfa AF: 0.131 Hom.: 762

Bravo AF: 0.147

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.99
DANN	Benign	0.77
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs4132476; hg19: chr9-121278291;