1-90410331-T-C

Variant names:

• chr1-90410331-T-C
• rs2136093
• ENST00000653744.1:n.171-9204A>G

Variant summary

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

The ENST00000653744.1(ENSG00000287372):​n.171-9204A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,008 control chromosomes in the GnomAD database, including 28,767 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 0.60 (28767 hom., cov: 33)
• Consequence: ENSG00000287372 ENST00000653744.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243

Genes affected

ENSG00000287372 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.699 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
ENSG00000287372	ENST00000653744.1	n.171-9204A>G		intron_variant	Intron 1 of 2
ENSG00000287372	ENST00000655087.1	n.420-9204A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91260 AN: 151890 Hom.: 28764 Cov.: 33

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.601 AC: 91284 AN: 152008 Hom.: 28767 Cov.: 33 AF XY: 0.595 AC XY: 44219 AN XY: 74304

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.638

Alfa AF: 0.651 Hom.: 19915

Bravo AF: 0.598

Asia WGS AF: 0.413 AC: 1444 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	6.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2136093; hg19: chr1-90875888;