rs7690819

Variant names:

• chr4-111199502-A-G
• rs7690819
• ENST00000681682.1:n.616+82230A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-111199502-A-G
• chr4-111199502-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000681682.1(ENSG00000288692):​n.616+82230A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,038 control chromosomes in the GnomAD database, including 13,443 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 0.41 (13443 hom., cov: 32)
• Consequence: ENSG00000288692 ENST00000681682.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

Genes affected

ENSG00000288692 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.462 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
ENSG00000288692	ENST00000681682.1	n.616+82230A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62862 AN: 151920 Hom.: 13433 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.414 AC: 62902 AN: 152038 Hom.: 13443 Cov.: 32 AF XY: 0.412 AC XY: 30624 AN XY: 74302

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.382

Alfa AF: 0.445 Hom.: 10265

Bravo AF: 0.401

Asia WGS AF: 0.432 AC: 1498 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	6.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7690819; hg19: chr4-112120658;