chr2-188727157-G-A

Variant names:

• chr2-188727157-G-A
• rs1916961
• ENST00000431708.1:n.218+19267C>T

Variant summary

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

The ENST00000431708.1(ENSG00000223523):​n.218+19267C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 151,950 control chromosomes in the GnomAD database, including 61,159 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 0.90 (61159 hom., cov: 31)
• Consequence: ENSG00000223523 ENST00000431708.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 5 publications found

Genes affected

ENSG00000223523 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373790	XR_923685.3	n.112-11435G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223523	ENST00000431708.1	n.218+19267C>T		intron_variant	Intron 2 of 7	3

Frequencies

GnomAD3 genomes AF: 0.896 AC: 135977 AN: 151832 Hom.: 61122 Cov.: 31

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.895 AC: 136070 AN: 151950 Hom.: 61159 Cov.: 31 AF XY: 0.896 AC XY: 66561 AN XY: 74286

African (AFR) AF: 0.836 AC: 34662 AN: 41474

American (AMR) AF: 0.913 AC: 13923 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2937 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5155 AN: 5158

South Asian (SAS) AF: 0.977 AC: 4717 AN: 4826

European-Finnish (FIN) AF: 0.914 AC: 9688 AN: 10598

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.913 AC: 61931 AN: 67868

Other (OTH) AF: 0.903 AC: 1905 AN: 2110

Alfa AF: 0.905 Hom.: 193059

Bravo AF: 0.892

Asia WGS AF: 0.981 AC: 3410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.17
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs1916961; hg19: chr2-189591884;