rs1407707

Variant names:

• chr1-188093118-T-C
• rs1407707
• ENST00000648838.2:n.455-4021T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-188093118-T-C
• chr1-188093118-T-G

Variant summary

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

The ENST00000648838.2(ENSG00000285894):​n.455-4021T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,954 control chromosomes in the GnomAD database, including 12,081 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 0.38 (12081 hom., cov: 31)
• Consequence: ENSG00000285894 ENST00000648838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38

Genes affected

ENSG00000285894 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 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
ENSG00000285894	ENST00000648838.2	n.455-4021T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57661 AN: 151836 Hom.: 12069 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.380 AC: 57704 AN: 151954 Hom.: 12081 Cov.: 31 AF XY: 0.389 AC XY: 28851 AN XY: 74240

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.377

Alfa AF: 0.403 Hom.: 1621

Bravo AF: 0.381

Asia WGS AF: 0.380 AC: 1324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.13
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1407707; hg19: chr1-188062249;