XR_007060868.1:n.1398-1737G>A

Variant names:

• chr8-27595330-G-A
• rs17466684
• ENST00000774578.1:n.170-1737G>A

Variant summary

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

The XR_007060868.1(LOC124901919):​n.1398-1737G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,068 control chromosomes in the GnomAD database, including 2,074 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 0.15 (2074 hom., cov: 32)
• Consequence: LOC124901919 XR_007060868.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 27 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=-0.56).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774578.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300853	ENST00000774578.1		n.170-1737G>A		intron	N/A
	ENSG00000300853	ENST00000774579.1		n.285-1737G>A		intron	N/A
	ENSG00000300853	ENST00000774580.1		n.129-1737G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22799 AN: 151950 Hom.: 2064 Cov.: 32

Gnomad AFR AF: 0.0557

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.150 AC: 22824 AN: 152068 Hom.: 2074 Cov.: 32 AF XY: 0.154 AC XY: 11450 AN XY: 74304

African (AFR) AF: 0.0555 AC: 2305 AN: 41526

American (AMR) AF: 0.219 AC: 3345 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3470

East Asian (EAS) AF: 0.147 AC: 757 AN: 5152

South Asian (SAS) AF: 0.154 AC: 740 AN: 4812

European-Finnish (FIN) AF: 0.241 AC: 2538 AN: 10544

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12292 AN: 67972

Other (OTH) AF: 0.138 AC: 291 AN: 2112

Alfa AF: 0.162 Hom.: 4630

Bravo AF: 0.143

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	1.1
DANN	Benign	0.80
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs17466684; hg19: chr8-27452847;