chr22-27153180-C-T

Variant names:

• chr22-27153180-C-T
• rs5997184
• ENST00000430468.1:n.53-6278C>T

Variant summary

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

The ENST00000430468.1(ENSG00000231405):​n.53-6278C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 143,956 control chromosomes in the GnomAD database, including 5,873 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 0.21 (5873 hom., cov: 28)
• Consequence: ENSG00000231405 ENST00000430468.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 1 publications found

Genes affected

ENSG00000231405 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231405	ENST00000430468.1	n.53-6278C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.209 AC: 30087 AN: 143914 Hom.: 5864 Cov.: 28

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0897

Gnomad EAS AF: 0.0554

Gnomad SAS AF: 0.0394

Gnomad FIN AF: 0.0798

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.0936

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.209 AC: 30117 AN: 143956 Hom.: 5873 Cov.: 28 AF XY: 0.203 AC XY: 14202 AN XY: 69814

African (AFR) AF: 0.520 AC: 20135 AN: 38714

American (AMR) AF: 0.127 AC: 1825 AN: 14350

Ashkenazi Jewish (ASJ) AF: 0.0897 AC: 304 AN: 3388

East Asian (EAS) AF: 0.0556 AC: 273 AN: 4912

South Asian (SAS) AF: 0.0386 AC: 175 AN: 4528

European-Finnish (FIN) AF: 0.0798 AC: 692 AN: 8676

Middle Eastern (MID) AF: 0.134 AC: 36 AN: 268

European-Non Finnish (NFE) AF: 0.0936 AC: 6198 AN: 66220

Other (OTH) AF: 0.174 AC: 348 AN: 2000

Alfa AF: 0.203 Hom.: 1019

Bravo AF: 0.227

Asia WGS AF: 0.0980 AC: 340 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.26
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs5997184; hg19: chr22-27549141;