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:53614):

ENSG00000288563 (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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507916.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251095	ENST00000507916.6	TSL:3	n.255+276A>T		intron	N/A
	ENSG00000251095	ENST00000508021.5	TSL:4	n.447+276A>T		intron	N/A
	ENSG00000251095	ENST00000513572.4	TSL:3	n.302+276A>T		intron	N/A

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 v4.9

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;