ENST00000437243.2:n.223+8001C>T

Variant names:

• chr2-173348166-G-A
• rs1550623
• ENST00000437243.2:n.223+8001C>T

Variant summary

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

The ENST00000437243.2(ENSG00000293276):​n.223+8001C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,096 control chromosomes in the GnomAD database, including 49,762 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 0.81 (49762 hom., cov: 32)
• Consequence: ENSG00000293276 ENST00000437243.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 74 publications found

Genes affected

ENSG00000293276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000437243.2. 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
	ENSG00000293276	ENST00000437243.2	TSL:3	n.223+8001C>T		intron	N/A
	ENSG00000293276	ENST00000809557.1		n.886+5517C>T		intron	N/A
	ENSG00000293276	ENST00000809558.1		n.930+5517C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122405 AN: 151978 Hom.: 49722 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.818

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.805 AC: 122491 AN: 152096 Hom.: 49762 Cov.: 32 AF XY: 0.807 AC XY: 59990 AN XY: 74338

African (AFR) AF: 0.705 AC: 29198 AN: 41438

American (AMR) AF: 0.782 AC: 11951 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3040 AN: 3472

East Asian (EAS) AF: 0.991 AC: 5141 AN: 5190

South Asian (SAS) AF: 0.882 AC: 4255 AN: 4822

European-Finnish (FIN) AF: 0.847 AC: 8948 AN: 10568

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57164 AN: 68004

Other (OTH) AF: 0.819 AC: 1729 AN: 2112

Alfa AF: 0.828 Hom.: 123472

Bravo AF: 0.793

Asia WGS AF: 0.926 AC: 3222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.8
DANN	Benign	0.30
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs1550623; hg19: chr2-174212894;