rs1930243

Variant names:

• chr9-100353890-G-A
• rs1930243
• ENST00000757903.1:n.560-107G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-100353890-G-A
• chr9-100353890-G-T

Variant summary

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

The ENST00000757903.1(ENSG00000298775):​n.560-107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 152,070 control chromosomes in the GnomAD database, including 32,275 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 0.63 (32275 hom., cov: 32)
• Consequence: ENSG00000298775 ENST00000757903.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 4 publications found

Genes affected

ENSG00000298775 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376177	NR_188637.1	n.533-107G>A		intron_variant	Intron 1 of 3
LOC105376177	NR_188638.1	n.533-107G>A		intron_variant	Intron 1 of 4
LOC105376177	NR_188639.1	n.533-107G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298775	ENST00000757903.1	n.560-107G>A		intron_variant	Intron 1 of 2
ENSG00000298775	ENST00000757904.1	n.615-107G>A		intron_variant	Intron 1 of 3
ENSG00000298775	ENST00000757905.1	n.615-107G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95935 AN: 151952 Hom.: 32225 Cov.: 32

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.632 AC: 96051 AN: 152070 Hom.: 32275 Cov.: 32 AF XY: 0.638 AC XY: 47438 AN XY: 74328

African (AFR) AF: 0.829 AC: 34410 AN: 41488

American (AMR) AF: 0.677 AC: 10348 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2020 AN: 3470

East Asian (EAS) AF: 0.894 AC: 4627 AN: 5178

South Asian (SAS) AF: 0.755 AC: 3640 AN: 4818

European-Finnish (FIN) AF: 0.542 AC: 5714 AN: 10540

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33566 AN: 67974

Other (OTH) AF: 0.608 AC: 1286 AN: 2114

Alfa AF: 0.595 Hom.: 4242

Bravo AF: 0.648

Asia WGS AF: 0.792 AC: 2753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.77
DANN	Benign	0.77
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1930243; hg19: chr9-103116172;