chr8-19245054-G-A

Position:

• chr8-19245054-G-A

Variant summary

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

The NR_038919.1(LOC100128993):​n.375+94C>T 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 0.0723 in 152,142 control chromosomes in the GnomAD database, including 545 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 0.072 (545 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LOC100128993 NR_038919.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100128993	NR_038919.1	n.375+94C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000520920.5	n.281+1655C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000654435.1	n.434C>T		non_coding_transcript_exon_variant	1/1
	ENST00000517949.5	n.342+94C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 10977 AN: 152024 Hom.: 541 Cov.: 33

Gnomad AFR AF: 0.0598

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0862

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.0703

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 578 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 266

Gnomad4 FIN exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0723 AC: 10994 AN: 152142 Hom.: 545 Cov.: 33 AF XY: 0.0765 AC XY: 5686 AN XY: 74370

Gnomad4 AFR AF: 0.0597

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.0585

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.0860

Gnomad4 FIN AF: 0.0726

Gnomad4 NFE AF: 0.0548

Gnomad4 OTH AF: 0.0691

Alfa AF: 0.0651 Hom.: 90

Bravo AF: 0.0777

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11787341; hg19: chr8-19102564;