rs4269515

Variant names:

• chr8-106896781-A-G
• rs4269515
• ENST00000766414.1:n.179-28364A>G

Variant summary

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

The ENST00000766414.1(ENSG00000299790):​n.179-28364A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 151,996 control chromosomes in the GnomAD database, including 1,767 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 0.13 (1767 hom., cov: 32)
• Consequence: ENSG00000299790 ENST00000766414.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 3 publications found

Genes affected

ENSG00000299790 (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 (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902066	XR_007061180.1	n.110-490A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299790	ENST00000766414.1	n.179-28364A>G		intron_variant	Intron 1 of 1
ENSG00000299790	ENST00000766415.1	n.144+4695A>G		intron_variant	Intron 1 of 1
ENSG00000299790	ENST00000766416.1	n.173-490A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20124 AN: 151876 Hom.: 1760 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0860

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.0764

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.133 AC: 20159 AN: 151996 Hom.: 1767 Cov.: 32 AF XY: 0.136 AC XY: 10116 AN XY: 74280

African (AFR) AF: 0.182 AC: 7551 AN: 41494

American (AMR) AF: 0.148 AC: 2248 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0860 AC: 298 AN: 3464

East Asian (EAS) AF: 0.388 AC: 1991 AN: 5138

South Asian (SAS) AF: 0.280 AC: 1348 AN: 4818

European-Finnish (FIN) AF: 0.0764 AC: 810 AN: 10606

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0814 AC: 5533 AN: 67938

Other (OTH) AF: 0.122 AC: 257 AN: 2114

Alfa AF: 0.101 Hom.: 3931

Bravo AF: 0.139

Asia WGS AF: 0.266 AC: 925 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	0.21
DANN	Benign	0.50
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4269515; hg19: chr8-107909009;