rs10464815

Variant names:

• chr8-100795923-A-C
• rs10464815
• ENST00000822257.1:n.154+84A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-100795923-A-C
• chr8-100795923-A-G

Variant summary

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

The ENST00000822257.1(ENSG00000306968):​n.154+84A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,172 control chromosomes in the GnomAD database, including 1,134 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 0.10 (1134 hom., cov: 31)
• Consequence: ENSG00000306968 ENST00000822257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 1 publications found

Genes affected

ENSG00000306968 (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 = 0.303 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
ENSG00000306968	ENST00000822257.1	n.154+84A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15732 AN: 152054 Hom.: 1126 Cov.: 31

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.0563

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.104 AC: 15780 AN: 152172 Hom.: 1134 Cov.: 31 AF XY: 0.107 AC XY: 7988 AN XY: 74398

African (AFR) AF: 0.143 AC: 5919 AN: 41506

American (AMR) AF: 0.191 AC: 2923 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3470

East Asian (EAS) AF: 0.316 AC: 1632 AN: 5164

South Asian (SAS) AF: 0.0825 AC: 397 AN: 4812

European-Finnish (FIN) AF: 0.0563 AC: 598 AN: 10618

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0561 AC: 3813 AN: 67998

Other (OTH) AF: 0.109 AC: 230 AN: 2110

Alfa AF: 0.0579 Hom.: 81

Bravo AF: 0.118

Asia WGS AF: 0.177 AC: 615 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	1.5
DANN	Benign	0.73
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs10464815; hg19: chr8-101808151;