8-95173122-C-T

Position:

• chr8-95173122-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.95173122C>T		intergenic_region
LOC124901982	XR_007061015.1	n.1835-8890C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.272

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17668689; hg19: chr8-96185350;