2-204065803-G-C

Variant names:

• chr2-204065803-G-C
• rs10497876
• ENST00000425328.1:n.98G>C

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000235951 ENST00000425328.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 1 publications found

Genes affected

ENSG00000235951 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 91 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100419685		n.204065803G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235951	ENST00000425328.1	n.98G>C		non_coding_transcript_exon_variant	Exon 1 of 2	6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 136

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 18

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.0433 AC: 1799 AN: 41568

American (AMR) AF: 0.0310 AC: 474 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00806 AC: 28 AN: 3472

East Asian (EAS) AF: 0.0150 AC: 78 AN: 5188

South Asian (SAS) AF: 0.0434 AC: 209 AN: 4818

European-Finnish (FIN) AF: 0.00838 AC: 89 AN: 10616

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0225 AC: 1530 AN: 68038

Other (OTH) AF: 0.0313 AC: 66 AN: 2110

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
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10497876; hg19: chr2-204930526;