4-99088976-C-T

Position:

• chr4-99088976-C-T

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.120C>T 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 0.38 in 434,456 control chromosomes in the GnomAD database, including 35,326 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 0.34 (10212 hom., cov: 33)
  • Exomes 𝑓: 0.40 (25114 hom.)
• Consequence: ENSG00000246090 ENST00000500358.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.120C>T		non_coding_transcript_exon_variant	1/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.120C>T		non_coding_transcript_exon_variant	1/10	1
ENSG00000246090	ENST00000499178.2	n.26C>T		non_coding_transcript_exon_variant	1/3	3
ENSG00000246090	ENST00000661393.1	n.117C>T		non_coding_transcript_exon_variant	1/10

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51188 AN: 151760 Hom.: 10206 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.349

GnomAD4 exome AF: 0.403 AC: 113952 AN: 282576 Hom.: 25114 Cov.: 0 AF XY: 0.409 AC XY: 60207 AN XY: 147168

Gnomad4 AFR exome AF: 0.132

Gnomad4 AMR exome AF: 0.327

Gnomad4 ASJ exome AF: 0.397

Gnomad4 EAS exome AF: 0.116

Gnomad4 SAS exome AF: 0.513

Gnomad4 FIN exome AF: 0.444

Gnomad4 NFE exome AF: 0.441

Gnomad4 OTH exome AF: 0.390

GnomAD4 genome AF: 0.337 AC: 51194 AN: 151880 Hom.: 10212 Cov.: 33 AF XY: 0.340 AC XY: 25223 AN XY: 74214

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.352

Alfa AF: 0.400 Hom.: 9736

Bravo AF: 0.313

Asia WGS AF: 0.373 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.1
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2851301; hg19: chr4-100010127;