rs10504216

Variant names:

• chr8-57068911-G-A
• rs10504216
• ENST00000798676.1:n.191-12271G>A

Variant summary

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

The ENST00000798676.1(ENSG00000303990):​n.191-12271G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0982 in 152,170 control chromosomes in the GnomAD database, including 886 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 0.098 (886 hom., cov: 33)
• Consequence: ENSG00000303990 ENST00000798676.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234
• Publications: 4 publications found

Genes affected

ENSG00000303990 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 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
ENSG00000303990	ENST00000798676.1	n.191-12271G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0982 AC: 14930 AN: 152054 Hom.: 883 Cov.: 33

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0711

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0982 AC: 14937 AN: 152170 Hom.: 886 Cov.: 33 AF XY: 0.101 AC XY: 7479 AN XY: 74406

African (AFR) AF: 0.0300 AC: 1245 AN: 41556

American (AMR) AF: 0.102 AC: 1553 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3468

East Asian (EAS) AF: 0.142 AC: 737 AN: 5174

South Asian (SAS) AF: 0.0710 AC: 342 AN: 4820

European-Finnish (FIN) AF: 0.190 AC: 2014 AN: 10574

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8326 AN: 67982

Other (OTH) AF: 0.106 AC: 224 AN: 2110

Alfa AF: 0.119 Hom.: 1460

Bravo AF: 0.0915

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
DANN	Benign	0.42
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10504216; hg19: chr8-57981470;