1-102370387-T-C

Variant names:

• chr1-102370387-T-C
• rs10874598
• ENST00000447916.1:n.339+16818A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000447916.1(ENSG00000233359):​n.339+16818A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,034 control chromosomes in the GnomAD database, including 55,951 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 0.84 (55951 hom., cov: 31)
• Consequence: ENSG00000233359 ENST00000447916.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

Genes affected

ENSG00000233359 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 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
ENSG00000233359	ENST00000447916.1	n.339+16818A>G		intron_variant	Intron 4 of 5	3

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128056 AN: 151916 Hom.: 55936 Cov.: 31

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.843 AC: 128113 AN: 152034 Hom.: 55951 Cov.: 31 AF XY: 0.847 AC XY: 62977 AN XY: 74324

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.946

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.970

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.868

Alfa AF: 0.880 Hom.: 7097

Bravo AF: 0.824

Asia WGS AF: 0.908 AC: 3144 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10874598; hg19: chr1-102835943;