rs17128007

chr8-19225642-C-T

Variant summary

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

The NR_038919.1(LOC100128993):n.568+1526G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0342 in 152,210 control chromosomes in the GnomAD database, including 148 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 0.034 (148 hom., cov: 32)
• Consequence: LOC100128993 NR_038919.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

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 (AFR) allele frequency at 95% confidence interval = 0.0734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100128993	NR_038919.1	n.568+1526G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000520920.5	n.474+1526G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000517949.5	n.535+1526G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000518417.1	n.278+1526G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0342 AC: 5198 AN: 152092 Hom.: 148 Cov.: 32

Gnomad AFR AF: 0.0757

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0158

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0303

Gnomad FIN AF: 0.0294

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0174

Gnomad OTH AF: 0.0273

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

GnomAD4 genome AF: 0.0342 AC: 5201 AN: 152210 Hom.: 148 Cov.: 32 AF XY: 0.0343 AC XY: 2553 AN XY: 74412

Gnomad4 AFR AF: 0.0756

Gnomad4 AMR AF: 0.0158

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0300

Gnomad4 FIN AF: 0.0294

Gnomad4 NFE AF: 0.0174

Gnomad4 OTH AF: 0.0270

Alfa AF: 0.0260 Hom.: 14

Bravo AF: 0.0335

Asia WGS AF: 0.0170 AC: 58 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	0.063
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17128007; hg19: chr8-19083152;