chr2-180602462-A-C

Variant names:

• chr2-180602462-A-C
• rs11691504
• ENST00000429816.1:n.235T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000429816.1(ENSG00000225258):​n.235T>G 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 0.403 in 151,898 control chromosomes in the GnomAD database, including 14,364 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 0.40 (14364 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000225258 ENST00000429816.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 7 publications found

Genes affected

ENSG00000225258 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429816.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225258	ENST00000429816.1	TSL:3	n.235T>G		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000304108	ENST00000799803.1		n.161-6656A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61267 AN: 151780 Hom.: 14374 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.466

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

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.403 AC: 61260 AN: 151898 Hom.: 14364 Cov.: 32 AF XY: 0.399 AC XY: 29592 AN XY: 74224

African (AFR) AF: 0.171 AC: 7105 AN: 41472

American (AMR) AF: 0.435 AC: 6623 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1987 AN: 3470

East Asian (EAS) AF: 0.298 AC: 1533 AN: 5146

South Asian (SAS) AF: 0.324 AC: 1563 AN: 4818

European-Finnish (FIN) AF: 0.457 AC: 4822 AN: 10548

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35903 AN: 67890

Other (OTH) AF: 0.461 AC: 973 AN: 2112

Alfa AF: 0.472 Hom.: 7116

Bravo AF: 0.398

Asia WGS AF: 0.286 AC: 995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	8.2
DANN	Benign	0.73
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs11691504; hg19: chr2-181467189;