rs279452

Variant names:

• chr19-48549278-A-C
• rs279452
• ENST00000666424.1:n.967T>G

Your query was ambiguous. Multiple possible variants found:

• chr19-48549278-A-C
• chr19-48549278-A-G
• chr19-48549278-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000287603 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287603	ENST00000666424.1	n.967T>G		non_coding_transcript_exon_variant	Exon 3 of 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

African (AFR) AF: 0.519 AC: 21473 AN: 41374

American (AMR) AF: 0.202 AC: 3078 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 656 AN: 3468

East Asian (EAS) AF: 0.473 AC: 2368 AN: 5004

South Asian (SAS) AF: 0.0972 AC: 467 AN: 4806

European-Finnish (FIN) AF: 0.206 AC: 2178 AN: 10552

Middle Eastern (MID) AF: 0.276 AC: 80 AN: 290

European-Non Finnish (NFE) AF: 0.171 AC: 11604 AN: 67922

Other (OTH) AF: 0.246 AC: 518 AN: 2106

Alfa AF: 0.213 Hom.: 2586

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs279452; hg19: chr19-49052535;