chr2-227803606-C-A

Variant names:

• chr2-227803606-C-A
• rs13385901
• ENST00000411678.1:n.1767C>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong 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: ENSG00000229172 ENST00000411678.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 1 publications found

Genes affected

ENSG00000229172 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS2: High Homozygotes in GnomAd4 at 10 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411678.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229172	ENST00000411678.1	TSL:6	n.1767C>A		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 58

Other (OTH) AF: 0.00 AC: 0 AN: 6

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0212 AC: 499 AN: 23548

American (AMR) AF: 0.0188 AC: 149 AN: 7942

Ashkenazi Jewish (ASJ) AF: 0.00943 AC: 23 AN: 2438

East Asian (EAS) AF: 0.0204 AC: 69 AN: 3384

South Asian (SAS) AF: 0.0354 AC: 73 AN: 2060

European-Finnish (FIN) AF: 0.0232 AC: 110 AN: 4748

Middle Eastern (MID) AF: 0.00463 AC: 1 AN: 216

European-Non Finnish (NFE) AF: 0.00924 AC: 407 AN: 44046

Other (OTH) AF: 0.0135 AC: 17 AN: 1256

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.160 Hom.: 26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		-0.50

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13385901;

hg19: chr2-228668322;

COSMIC: COSV68736747;