8-95173122-C-T

Variant names:

• chr8-95173122-C-T
• rs17668689
• ENST00000812778.1:n.401+2244G>A

Variant summary

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

The ENST00000812778.1(ENSG00000305752):​n.401+2244G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,170 control chromosomes in the GnomAD database, including 4,811 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 0.24 (4811 hom., cov: 32)
• Consequence: ENSG00000305752 ENST00000812778.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 1 publications found

Genes affected

ENSG00000305752 (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 (NFE) 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
LOC124901982	XR_007061015.1	n.1835-8890C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305752	ENST00000812778.1	n.401+2244G>A		intron_variant	Intron 2 of 2
ENSG00000305765	ENST00000812840.1	n.177-1932C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36802 AN: 152052 Hom.: 4812 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.242 AC: 36817 AN: 152170 Hom.: 4811 Cov.: 32 AF XY: 0.237 AC XY: 17637 AN XY: 74406

African (AFR) AF: 0.161 AC: 6680 AN: 41524

American (AMR) AF: 0.206 AC: 3141 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1007 AN: 3468

East Asian (EAS) AF: 0.162 AC: 839 AN: 5182

South Asian (SAS) AF: 0.129 AC: 621 AN: 4830

European-Finnish (FIN) AF: 0.263 AC: 2779 AN: 10568

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20850 AN: 67996

Other (OTH) AF: 0.272 AC: 574 AN: 2114

Alfa AF: 0.171 Hom.: 483

Bravo AF: 0.238

Asia WGS AF: 0.158 AC: 550 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	1.4
DANN	Benign	0.58
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs17668689; hg19: chr8-96185350;