rs219553

Variant names:

• chr2-21354871-G-A
• rs219553
• ENST00000435237.1:n.120+133577G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-21354871-G-A
• chr2-21354871-G-C
• chr2-21354871-G-T

Variant summary

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

The ENST00000435237.1(ENSG00000231204):​n.120+133577G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,102 control chromosomes in the GnomAD database, including 12,091 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 0.34 (12091 hom., cov: 33)
• Consequence: ENSG00000231204 ENST00000435237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 11 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374318	XR_939801.3	n.3786-1706G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231204	ENST00000435237.1	n.120+133577G>A		intron_variant	Intron 1 of 5	3
ENSG00000231204	ENST00000451476.1	n.246+34377G>A		intron_variant	Intron 2 of 4	5
ENSG00000231204	ENST00000649482.1	n.204-1706G>A		intron_variant	Intron 2 of 6
ENSG00000231204	ENST00000653699.1	n.247-1706G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52288 AN: 151984 Hom.: 12069 Cov.: 33

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.344 AC: 52361 AN: 152102 Hom.: 12091 Cov.: 33 AF XY: 0.342 AC XY: 25437 AN XY: 74332

African (AFR) AF: 0.669 AC: 27724 AN: 41466

American (AMR) AF: 0.286 AC: 4368 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3470

East Asian (EAS) AF: 0.247 AC: 1277 AN: 5176

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4818

European-Finnish (FIN) AF: 0.205 AC: 2163 AN: 10568

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14095 AN: 67990

Other (OTH) AF: 0.307 AC: 650 AN: 2114

Alfa AF: 0.254 Hom.: 19796

Bravo AF: 0.363

Asia WGS AF: 0.253 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.63
DANN	Benign	0.30
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs219553; hg19: chr2-21577743;