rs1918425

Variant names:

• chr7-70906208-T-C
• rs1918425
• ENST00000760408.1:n.106+11481T>C

Variant summary

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

The ENST00000760408.1(ENSG00000299089):​n.106+11481T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 152,018 control chromosomes in the GnomAD database, including 16,380 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 0.46 (16380 hom., cov: 32)
• Consequence: ENSG00000299089 ENST00000760408.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 2 publications found

Genes affected

ENSG00000299089 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 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
ENSG00000299089	ENST00000760408.1	n.106+11481T>C		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69300 AN: 151900 Hom.: 16353 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.456 AC: 69369 AN: 152018 Hom.: 16380 Cov.: 32 AF XY: 0.449 AC XY: 33346 AN XY: 74302

African (AFR) AF: 0.574 AC: 23812 AN: 41468

American (AMR) AF: 0.407 AC: 6217 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1757 AN: 3466

East Asian (EAS) AF: 0.313 AC: 1614 AN: 5156

South Asian (SAS) AF: 0.364 AC: 1746 AN: 4800

European-Finnish (FIN) AF: 0.309 AC: 3266 AN: 10574

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29428 AN: 67976

Other (OTH) AF: 0.449 AC: 949 AN: 2112

Alfa AF: 0.446 Hom.: 51405

Bravo AF: 0.469

Asia WGS AF: 0.425 AC: 1477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.54
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1918425; hg19: chr7-70371194;