rs7690104

Variant names:

• chr4-114752803-G-A
• rs7690104

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.851

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.327

Alfa AF: 0.284 Hom.: 1514

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

Splicing

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

Publications

LitVar

Other links and lift over

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