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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929230	XR_001739327.2	n.2803-9311G>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231204	ENST00000435237.1	n.193+87978C>T		intron_variant	Intron 3 of 5	3
ENSG00000235537	ENST00000648747.1	n.1032-9311G>A		intron_variant	Intron 2 of 2
ENSG00000231204	ENST00000717099.1	n.555+52155C>T		intron_variant	Intron 5 of 6

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 v4.3

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;