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. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000285894 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648838.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285894	ENST00000648838.2		n.455-4021T>C		intron	N/A
	ENSG00000285894	ENST00000733149.1		n.164-4021T>C		intron	N/A

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

African (AFR) AF: 0.229 AC: 9487 AN: 41438

American (AMR) AF: 0.489 AC: 7467 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1327 AN: 3464

East Asian (EAS) AF: 0.524 AC: 2704 AN: 5164

South Asian (SAS) AF: 0.264 AC: 1270 AN: 4814

European-Finnish (FIN) AF: 0.509 AC: 5362 AN: 10536

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28650 AN: 67958

Other (OTH) AF: 0.377 AC: 796 AN: 2114

Alfa AF: 0.397 Hom.: 1647

Bravo AF: 0.381

Asia WGS AF: 0.380 AC: 1324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.13
DANN	Benign	0.30
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs1407707; hg19: chr1-188062249;