chr8-121493184-A-G

Variant names:

• chr8-121493184-A-G
• rs10505405
• ENST00000784704.1:n.285+19977A>G

Variant summary

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

The ENST00000784704.1(ENSG00000302156):​n.285+19977A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0401 in 152,204 control chromosomes in the GnomAD database, including 181 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 0.040 (181 hom., cov: 32)
• Consequence: ENSG00000302156 ENST00000784704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 1 publications found

Genes affected

ENSG00000302156 (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 (AFR) allele frequency at 95% confidence interval = 0.0728 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
ENSG00000302156	ENST00000784704.1	n.285+19977A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0401 AC: 6095 AN: 152086 Hom.: 180 Cov.: 32

Gnomad AFR AF: 0.0749

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0423

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.00490

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0231

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0401 AC: 6101 AN: 152204 Hom.: 181 Cov.: 32 AF XY: 0.0403 AC XY: 3002 AN XY: 74432

African (AFR) AF: 0.0750 AC: 3112 AN: 41514

American (AMR) AF: 0.0525 AC: 803 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0423 AC: 147 AN: 3472

East Asian (EAS) AF: 0.0338 AC: 175 AN: 5174

South Asian (SAS) AF: 0.0228 AC: 110 AN: 4828

European-Finnish (FIN) AF: 0.00490 AC: 52 AN: 10610

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0231 AC: 1571 AN: 67996

Other (OTH) AF: 0.0345 AC: 73 AN: 2114

Alfa AF: 0.0276 Hom.: 114

Bravo AF: 0.0448

Asia WGS AF: 0.0530 AC: 184 AN: 3476

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	0.48
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs10505405; hg19: chr8-122505424;