chr9-104928428-C-G

Variant names:

• chr9-104928428-C-G
• rs1800976
• ENST00000435915.1:n.359-354C>G

Variant summary

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

The ENST00000435915.1(ENSG00000226334):​n.359-354C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,554 control chromosomes in the GnomAD database, including 17,286 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 0.47 (17286 hom., cov: 31)
• Consequence: ENSG00000226334 ENST00000435915.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 26 publications found

Genes affected

ENSG00000226334 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376196	NR_188620.1	n.1122+518C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226334	ENST00000435915.1	n.359-354C>G		intron_variant	Intron 1 of 1	3
ENSG00000226334	ENST00000820514.1	n.1164+518C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.475 AC: 71931 AN: 151436 Hom.: 17279 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.475 AC: 71970 AN: 151554 Hom.: 17286 Cov.: 31 AF XY: 0.480 AC XY: 35506 AN XY: 74020

African (AFR) AF: 0.439 AC: 18178 AN: 41408

American (AMR) AF: 0.531 AC: 8079 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1981 AN: 3456

East Asian (EAS) AF: 0.433 AC: 2200 AN: 5080

South Asian (SAS) AF: 0.550 AC: 2631 AN: 4780

European-Finnish (FIN) AF: 0.560 AC: 5859 AN: 10460

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31326 AN: 67826

Other (OTH) AF: 0.479 AC: 1010 AN: 2110

Alfa AF: 0.463 Hom.: 2020

Bravo AF: 0.472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.0
DANN	Benign	0.79
PhyloP100		-0.14
PromoterAI		0.041	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1800976; hg19: chr9-107690709;