rs9421801

Variant names:

• chr10-47316507-T-C
• rs9421801
• ENST00000816238.1:n.214+103T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-47316507-T-C
• chr10-47316507-T-G

Variant summary

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

The ENST00000816238.1(ENSG00000306200):​n.214+103T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,138 control chromosomes in the GnomAD database, including 64,637 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 0.92 (64637 hom., cov: 30)
• Consequence: ENSG00000306200 ENST00000816238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 2 publications found

Genes affected

ENSG00000306200 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.936 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
ENSG00000306200	ENST00000816238.1	n.214+103T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.921 AC: 139978 AN: 152020 Hom.: 64586 Cov.: 30

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.914

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.921 AC: 140091 AN: 152138 Hom.: 64637 Cov.: 30 AF XY: 0.919 AC XY: 68318 AN XY: 74350

African (AFR) AF: 0.916 AC: 38024 AN: 41504

American (AMR) AF: 0.903 AC: 13809 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3157 AN: 3472

East Asian (EAS) AF: 0.743 AC: 3806 AN: 5122

South Asian (SAS) AF: 0.814 AC: 3921 AN: 4816

European-Finnish (FIN) AF: 0.963 AC: 10210 AN: 10606

Middle Eastern (MID) AF: 0.918 AC: 268 AN: 292

European-Non Finnish (NFE) AF: 0.942 AC: 64041 AN: 68008

Other (OTH) AF: 0.922 AC: 1947 AN: 2112

Alfa AF: 0.931 Hom.: 66119

Bravo AF: 0.917

Asia WGS AF: 0.788 AC: 2742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.6
DANN	Benign	0.87
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs9421801; hg19: chr10-48422855;