chr2-21617221-C-T

Variant names:

• chr2-21617221-C-T
• rs1117324
• ENST00000435237.1:n.193+87978C>T

Variant summary

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

The ENST00000435237.1(ENSG00000231204):​n.193+87978C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 152,064 control chromosomes in the GnomAD database, including 57,006 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 0.85 (57006 hom., cov: 31)
• Consequence: ENSG00000231204 ENST00000435237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719
• Publications: 12 publications found

Genes affected

ENSG00000231204 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435237.1. 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
	ENSG00000231204	ENST00000435237.1	TSL:3	n.193+87978C>T		intron	N/A
	ENSG00000235537	ENST00000648747.1		n.1032-9311G>A		intron	N/A
	ENSG00000231204	ENST00000717099.1		n.555+52155C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129032 AN: 151946 Hom.: 56991 Cov.: 31

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.977

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.849 AC: 129076 AN: 152064 Hom.: 57006 Cov.: 31 AF XY: 0.851 AC XY: 63268 AN XY: 74336

African (AFR) AF: 0.581 AC: 24063 AN: 41414

American (AMR) AF: 0.887 AC: 13555 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 3340 AN: 3472

East Asian (EAS) AF: 0.858 AC: 4405 AN: 5134

South Asian (SAS) AF: 0.945 AC: 4555 AN: 4818

European-Finnish (FIN) AF: 0.977 AC: 10360 AN: 10602

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.967 AC: 65794 AN: 68024

Other (OTH) AF: 0.866 AC: 1828 AN: 2112

Alfa AF: 0.936 Hom.: 117756

Bravo AF: 0.829

Asia WGS AF: 0.868 AC: 3019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.57
DANN	Benign	0.76
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs1117324; hg19: chr2-21840093;