ENST00000422118.1:n.179-1921A>C

Variant names:

• chr2-223502061-A-C
• rs721357
• ENST00000422118.1:n.179-1921A>C

Variant summary

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

The ENST00000422118.1(ENSG00000231189):​n.179-1921A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,016 control chromosomes in the GnomAD database, including 31,617 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 0.64 (31617 hom., cov: 33)
• Consequence: ENSG00000231189 ENST00000422118.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424
• Publications: 4 publications found

Genes affected

ENSG00000231189 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373907	NR_187972.1	n.204+2808A>C		intron_variant	Intron 2 of 4
LOC105373907	NR_187973.1	n.204+2808A>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231189	ENST00000422118.1	n.179-1921A>C		intron_variant	Intron 2 of 2	3
ENSG00000303770	ENST00000797088.1	n.189-18417T>G		intron_variant	Intron 2 of 3
ENSG00000303770	ENST00000797089.1	n.43-18417T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97611 AN: 151898 Hom.: 31599 Cov.: 33

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.642 AC: 97668 AN: 152016 Hom.: 31617 Cov.: 33 AF XY: 0.639 AC XY: 47485 AN XY: 74268

African (AFR) AF: 0.643 AC: 26669 AN: 41452

American (AMR) AF: 0.573 AC: 8749 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1951 AN: 3468

East Asian (EAS) AF: 0.622 AC: 3222 AN: 5178

South Asian (SAS) AF: 0.585 AC: 2809 AN: 4804

European-Finnish (FIN) AF: 0.637 AC: 6721 AN: 10544

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45457 AN: 67988

Other (OTH) AF: 0.614 AC: 1299 AN: 2116

Alfa AF: 0.653 Hom.: 120594

Bravo AF: 0.638

Asia WGS AF: 0.592 AC: 2057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.9
DANN	Benign	0.58
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs721357; hg19: chr2-224366779;