rs77878271

Positions:

• chr8-81483300-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The ENST00000524085.2(ENSG00000253859):​n.299-14617A>G variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.0191 in 474,530 control chromosomes in the GnomAD database, including 133 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 0.016 (35 hom., cov: 32)
  • Exomes 𝑓: 0.020 (98 hom.)
• Consequence: ENST00000524085.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.39

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0163 (2488/152258) while in subpopulation NFE AF= 0.0224 (1523/68004). AF 95% confidence interval is 0.0215. There are 35 homozygotes in gnomad4. There are 1291 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 35 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927118	XR_001745980.2	n.517+21326A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000524085.2	n.299-14617A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0163 AC: 2485 AN: 152140 Hom.: 35 Cov.: 32

Gnomad AFR AF: 0.00372

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00943

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0224

Gnomad OTH AF: 0.0139

GnomAD4 exome AF: 0.0204 AC: 6582 AN: 322272 Hom.: 98 Cov.: 5 AF XY: 0.0200 AC XY: 3331 AN XY: 166470

Gnomad4 AFR exome AF: 0.00307

Gnomad4 AMR exome AF: 0.00751

Gnomad4 ASJ exome AF: 0.0187

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00357

Gnomad4 FIN exome AF: 0.0604

Gnomad4 NFE exome AF: 0.0206

Gnomad4 OTH exome AF: 0.0190

GnomAD4 genome AF: 0.0163 AC: 2488 AN: 152258 Hom.: 35 Cov.: 32 AF XY: 0.0173 AC XY: 1291 AN XY: 74438

Gnomad4 AFR AF: 0.00370

Gnomad4 AMR AF: 0.00955

Gnomad4 ASJ AF: 0.0176

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00187

Gnomad4 FIN AF: 0.0532

Gnomad4 NFE AF: 0.0224

Gnomad4 OTH AF: 0.0137

Alfa AF: 0.0204 Hom.: 5

Bravo AF: 0.0130

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	19
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs77878271; hg19: chr8-82395535;