rs13385901

Positions:

• chr2-227803606-C-A

Variant summary

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

The ENST00000411678.1(ENSG00000229172):​n.1767C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.015 (10 hom., cov: 16)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000411678.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.015 (1353/90310) while in subpopulation SAS AF= 0.0354 (73/2060). AF 95% confidence interval is 0.0289. There are 10 homozygotes in gnomad4. There are 708 alleles in male gnomad4 subpopulation. Median coverage is 16. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 10 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000411678.1	n.1767C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0150 AC: 1351 AN: 90310 Hom.: 10 Cov.: 16

Gnomad AFR AF: 0.0212

Gnomad AMI AF: 0.00744

Gnomad AMR AF: 0.0186

Gnomad ASJ AF: 0.00943

Gnomad EAS AF: 0.0203

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.00431

Gnomad NFE AF: 0.00924

Gnomad OTH AF: 0.0135

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 70 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 48

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0150 AC: 1353 AN: 90310 Hom.: 10 Cov.: 16 AF XY: 0.0164 AC XY: 708 AN XY: 43180

Gnomad4 AFR AF: 0.0212

Gnomad4 AMR AF: 0.0188

Gnomad4 ASJ AF: 0.00943

Gnomad4 EAS AF: 0.0204

Gnomad4 SAS AF: 0.0354

Gnomad4 FIN AF: 0.0232

Gnomad4 NFE AF: 0.00924

Gnomad4 OTH AF: 0.0135

Alfa AF: 0.160 Hom.: 26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13385901; hg19: chr2-228668322; COSMIC: COSV68736747;