2-204065803-G-C

Position:

• chr2-204065803-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000425328.1(ENSG00000235951):​n.98G>C 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 0.0281 in 152,318 control chromosomes in the GnomAD database, including 91 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 0.028 (91 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000425328.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0281 (4280/152318) while in subpopulation SAS AF= 0.0434 (209/4818). AF 95% confidence interval is 0.0416. There are 91 homozygotes in gnomad4. There are 2080 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 91 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000425328.1	n.98G>C		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.0281 AC: 4275 AN: 152200 Hom.: 89 Cov.: 32

Gnomad AFR AF: 0.0434

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.00806

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.0431

Gnomad FIN AF: 0.00838

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0225

Gnomad OTH AF: 0.0273

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 156 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 86

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0281 AC: 4280 AN: 152318 Hom.: 91 Cov.: 32 AF XY: 0.0279 AC XY: 2080 AN XY: 74486

Gnomad4 AFR AF: 0.0433

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.00806

Gnomad4 EAS AF: 0.0150

Gnomad4 SAS AF: 0.0434

Gnomad4 FIN AF: 0.00838

Gnomad4 NFE AF: 0.0225

Gnomad4 OTH AF: 0.0313

Alfa AF: 0.00331 Hom.: 1

Bravo AF: 0.0302

Asia WGS AF: 0.0450 AC: 155 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	0.024
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497876; hg19: chr2-204930526;