chr19-28522014-T-C

Position:

• chr19-28522014-T-C

Variant summary

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

The NR_110759.1(LOC100420587):​n.657-55234A>G 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 0.226 in 151,242 control chromosomes in the GnomAD database, including 4,590 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 0.23 (4590 hom., cov: 31)
• Consequence: LOC100420587 NR_110759.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100420587	NR_110759.1	n.657-55234A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000589999.1	n.110-28991A>G		intron_variant, non_coding_transcript_variant		1
	ENST00000593065.5	n.178+13086A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34148 AN: 151122 Hom.: 4583 Cov.: 31

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.226 AC: 34181 AN: 151242 Hom.: 4590 Cov.: 31 AF XY: 0.226 AC XY: 16649 AN XY: 73810

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.221

Alfa AF: 0.169 Hom.: 5081

Bravo AF: 0.233

Asia WGS AF: 0.226 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8113142; hg19: chr19-29012921;