4-111199502-A-G

Variant names:

• chr4-111199502-A-G
• rs7690819
• ENST00000681682.2:n.616+82230A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000681682.2(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 ENST00000681682.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 4 publications found

Genes affected

ENSG00000288692 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000681682.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288692	ENST00000681682.2		n.616+82230A>G		intron	N/A

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

African (AFR) AF: 0.349 AC: 14491 AN: 41498

American (AMR) AF: 0.348 AC: 5316 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1150 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2108 AN: 5156

South Asian (SAS) AF: 0.467 AC: 2251 AN: 4824

European-Finnish (FIN) AF: 0.439 AC: 4637 AN: 10558

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31695 AN: 67954

Other (OTH) AF: 0.382 AC: 805 AN: 2110

Alfa AF: 0.436 Hom.: 16596

Bravo AF: 0.401

Asia WGS AF: 0.432 AC: 1498 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	6.4
DANN	Benign	0.81
PhyloP100		0.0040

Splicing

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

Other links and lift over

dbSNP: rs7690819; hg19: chr4-112120658;