rs4098804

Variant names:

• chr10-52826568-G-A
• rs4098804
• ENST00000816733.1:n.692+15871G>A

Variant summary

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

The ENST00000816733.1(ENSG00000306279):​n.692+15871G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,966 control chromosomes in the GnomAD database, including 3,425 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 0.20 (3425 hom., cov: 32)
• Consequence: ENSG00000306279 ENST00000816733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 3 publications found

Genes affected

ENSG00000306279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.296 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
ENSG00000306279	ENST00000816733.1	n.692+15871G>A		intron_variant	Intron 3 of 3
ENSG00000306279	ENST00000816737.1	n.219-477G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30136 AN: 151850 Hom.: 3420 Cov.: 32

Gnomad AFR AF: 0.0996

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.198 AC: 30145 AN: 151966 Hom.: 3425 Cov.: 32 AF XY: 0.200 AC XY: 14874 AN XY: 74224

African (AFR) AF: 0.0995 AC: 4130 AN: 41502

American (AMR) AF: 0.303 AC: 4609 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 664 AN: 3470

East Asian (EAS) AF: 0.251 AC: 1295 AN: 5154

South Asian (SAS) AF: 0.208 AC: 1002 AN: 4816

European-Finnish (FIN) AF: 0.197 AC: 2079 AN: 10552

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15722 AN: 67938

Other (OTH) AF: 0.210 AC: 443 AN: 2108

Alfa AF: 0.221 Hom.: 684

Bravo AF: 0.204

Asia WGS AF: 0.199 AC: 693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.54
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs4098804; hg19: chr10-54586328;