chr19-48549278-A-C

Position:

• chr19-48549278-A-C

Variant summary

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

The ENST00000666424.1(ENSG00000287603):​n.967T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 151,670 control chromosomes in the GnomAD database, including 7,988 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 0.28 (7988 hom., cov: 31)
• Consequence: ENSG00000287603 ENST00000666424.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

ENSG00000287603 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.48549278A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287603	ENST00000666424.1	n.967T>G		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42406 AN: 151552 Hom.: 7963 Cov.: 31

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.0983

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.280 AC: 42475 AN: 151670 Hom.: 7988 Cov.: 31 AF XY: 0.280 AC XY: 20771 AN XY: 74112

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.0972

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.246

Alfa AF: 0.193 Hom.: 1264

Bravo AF: 0.297

Asia WGS AF: 0.299 AC: 1038 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs279452; hg19: chr19-49052535;