4-89691681-A-T

Variant names:

• chr4-89691681-A-T
• rs3857049
• ENST00000507916.6:n.255+276A>T

Variant summary

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

The ENST00000507916.6(ENSG00000251095):​n.255+276A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0739 in 152,182 control chromosomes in the GnomAD database, including 1,189 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 0.074 (1189 hom., cov: 32)
• Consequence: ENSG00000251095 ENST00000507916.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471
• Publications: 2 publications found

Genes affected

ENSG00000251095 (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 (EAS) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900602	XR_001741764.2	n.5620-224A>T		intron_variant	Intron 2 of 2
LOC124900602	XR_007058465.1	n.9901+276A>T		intron_variant	Intron 1 of 1
LOC124900602	XR_007058466.1	n.9901+276A>T		intron_variant	Intron 1 of 2
LOC124900602	XR_938983.2	n.5619+276A>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251095	ENST00000507916.6	n.255+276A>T		intron_variant	Intron 2 of 2	3
ENSG00000251095	ENST00000508021.5	n.447+276A>T		intron_variant	Intron 4 of 4	4
ENSG00000251095	ENST00000513572.4	n.302+276A>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0738 AC: 11222 AN: 152064 Hom.: 1182 Cov.: 32

Gnomad AFR AF: 0.0684

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0856

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0169

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0739 AC: 11250 AN: 152182 Hom.: 1189 Cov.: 32 AF XY: 0.0803 AC XY: 5971 AN XY: 74400

African (AFR) AF: 0.0685 AC: 2847 AN: 41532

American (AMR) AF: 0.167 AC: 2546 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0856 AC: 297 AN: 3468

East Asian (EAS) AF: 0.515 AC: 2657 AN: 5158

South Asian (SAS) AF: 0.155 AC: 745 AN: 4820

European-Finnish (FIN) AF: 0.0758 AC: 804 AN: 10610

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0169 AC: 1149 AN: 68010

Other (OTH) AF: 0.0900 AC: 190 AN: 2112

Alfa AF: 0.0406 Hom.: 57

Bravo AF: 0.0867

Asia WGS AF: 0.337 AC: 1168 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	2.3
DANN	Benign	0.52
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs3857049; hg19: chr4-90612832;