chr5-143561127-T-A

Variant names:

• chr5-143561127-T-A
• rs11955681
• ENST00000514942.2:n.219-179T>A

Variant summary

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

The ENST00000514942.2(ENSG00000251205):​n.219-179T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0958 in 152,262 control chromosomes in the GnomAD database, including 1,025 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 0.096 (1025 hom., cov: 32)
• Consequence: ENSG00000251205 ENST00000514942.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 3 publications found

Genes affected

ENSG00000251205 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378209	XR_944375.1	n.-186T>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251205	ENST00000514942.2	n.219-179T>A		intron_variant	Intron 1 of 3	5
ENSG00000251205	ENST00000661617.1	n.242-179T>A		intron_variant	Intron 1 of 4
ENSG00000251205	ENST00000833525.1	n.116-179T>A		intron_variant	Intron 1 of 4
ENSG00000251205	ENST00000833526.1	n.78-179T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14601 AN: 152144 Hom.: 1024 Cov.: 32

Gnomad AFR AF: 0.0253

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0721

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0250

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.0821

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

GnomAD4 genome AF: 0.0958 AC: 14594 AN: 152262 Hom.: 1025 Cov.: 32 AF XY: 0.0932 AC XY: 6939 AN XY: 74452

African (AFR) AF: 0.0252 AC: 1049 AN: 41550

American (AMR) AF: 0.0721 AC: 1103 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3470

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.0242 AC: 117 AN: 4828

European-Finnish (FIN) AF: 0.152 AC: 1614 AN: 10604

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10226 AN: 67994

Other (OTH) AF: 0.0813 AC: 172 AN: 2116

Alfa AF: 0.0579 Hom.: 69

Bravo AF: 0.0908

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	2.1
DANN	Benign	0.88
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs11955681; hg19: chr5-142940692;