rs2301241

Variant names:

• chr9-110257228-G-A
• rs2301241
• ENST00000786399.1:n.283+253G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-110257228-G-A
• chr9-110257228-G-C
• chr9-110257228-G-T

Variant summary

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

The ENST00000786399.1(ENSG00000302400):​n.283+253G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 151,900 control chromosomes in the GnomAD database, including 25,610 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 0.58 (25610 hom., cov: 30)
• Consequence: ENSG00000302400 ENST00000786399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 27 publications found

Genes affected

ENSG00000302400 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 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
ENSG00000302400	ENST00000786399.1	n.283+253G>A		intron_variant	Intron 1 of 4
ENSG00000302400	ENST00000786400.1	n.253+253G>A		intron_variant	Intron 1 of 3
ENSG00000302400	ENST00000786401.1	n.320+253G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87347 AN: 151782 Hom.: 25599 Cov.: 30

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.575 AC: 87402 AN: 151900 Hom.: 25610 Cov.: 30 AF XY: 0.575 AC XY: 42684 AN XY: 74218

African (AFR) AF: 0.555 AC: 22975 AN: 41424

American (AMR) AF: 0.657 AC: 10031 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1945 AN: 3472

East Asian (EAS) AF: 0.751 AC: 3861 AN: 5144

South Asian (SAS) AF: 0.681 AC: 3266 AN: 4798

European-Finnish (FIN) AF: 0.453 AC: 4775 AN: 10530

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38641 AN: 67938

Other (OTH) AF: 0.547 AC: 1157 AN: 2114

Alfa AF: 0.578 Hom.: 97035

Bravo AF: 0.592

Asia WGS AF: 0.686 AC: 2382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.40
DANN	Benign	0.73
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2301241; hg19: chr9-113019508;