8-27596276-C-G

Variant names:

• chr8-27596276-C-G
• rs17057444
• ENST00000774578.1:n.170-791C>G

Variant summary

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

The ENST00000774578.1(ENSG00000300853):​n.170-791C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0457 in 152,282 control chromosomes in the GnomAD database, including 192 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 0.046 (192 hom., cov: 31)
• Consequence: ENSG00000300853 ENST00000774578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848
• Publications: 2 publications found

Genes affected

ENSG00000300853 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901919	XR_007060868.1	n.1398-791C>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300853	ENST00000774578.1	n.170-791C>G		intron_variant	Intron 1 of 1
ENSG00000300853	ENST00000774579.1	n.285-791C>G		intron_variant	Intron 1 of 1
ENSG00000300853	ENST00000774580.1	n.129-791C>G		intron_variant	Intron 1 of 1
ENSG00000300853	ENST00000774581.1	n.403-791C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0456 AC: 6942 AN: 152164 Hom.: 191 Cov.: 31

Gnomad AFR AF: 0.0735

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0380

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0147

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.0182

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0408

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0457 AC: 6959 AN: 152282 Hom.: 192 Cov.: 31 AF XY: 0.0439 AC XY: 3265 AN XY: 74456

African (AFR) AF: 0.0737 AC: 3060 AN: 41540

American (AMR) AF: 0.0380 AC: 581 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3472

East Asian (EAS) AF: 0.0147 AC: 76 AN: 5168

South Asian (SAS) AF: 0.0137 AC: 66 AN: 4826

European-Finnish (FIN) AF: 0.0182 AC: 193 AN: 10626

Middle Eastern (MID) AF: 0.0240 AC: 7 AN: 292

European-Non Finnish (NFE) AF: 0.0408 AC: 2774 AN: 68034

Other (OTH) AF: 0.0454 AC: 96 AN: 2114

Alfa AF: 0.00529 Hom.: 1

Bravo AF: 0.0487

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.71
DANN	Benign	0.40
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs17057444; hg19: chr8-27453793;