rs7690104

Variant names:

• chr4-114752803-G-A
• rs7690104
• ENST00000830399.1:n.180+25108G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-114752803-G-A
• chr4-114752803-G-T

Variant summary

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

The ENST00000830399.1(ENSG00000308009):​n.180+25108G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,050 control chromosomes in the GnomAD database, including 8,143 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 0.32 (8143 hom., cov: 33)
• Consequence: ENSG00000308009 ENST00000830399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.851
• Publications: 3 publications found

Genes affected

ENSG00000308009 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.384 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
ENSG00000308009	ENST00000830399.1	n.180+25108G>A		intron_variant	Intron 1 of 2
ENSG00000308009	ENST00000830400.1	n.172+25108G>A		intron_variant	Intron 1 of 1
ENSG00000308009	ENST00000830401.1	n.200+25108G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48791 AN: 151932 Hom.: 8126 Cov.: 33

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.321 AC: 48861 AN: 152050 Hom.: 8143 Cov.: 33 AF XY: 0.323 AC XY: 24029 AN XY: 74310

African (AFR) AF: 0.248 AC: 10286 AN: 41472

American (AMR) AF: 0.392 AC: 5990 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1121 AN: 3468

East Asian (EAS) AF: 0.302 AC: 1554 AN: 5154

South Asian (SAS) AF: 0.397 AC: 1914 AN: 4816

European-Finnish (FIN) AF: 0.315 AC: 3331 AN: 10562

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23639 AN: 67984

Other (OTH) AF: 0.327 AC: 689 AN: 2108

Alfa AF: 0.283 Hom.: 1536

Bravo AF: 0.321

Asia WGS AF: 0.370 AC: 1285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	7.3
DANN	Benign	0.65
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs7690104; hg19: chr4-115673959; COSMIC: COSV50779961;