chr4-89679620-G-A

Variant names:

• chr4-89679620-G-A
• rs3857046
• ENST00000506864.5:n.472-11665G>A

Variant summary

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

The ENST00000506864.5(ENSG00000251095):​n.472-11665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,130 control chromosomes in the GnomAD database, including 3,001 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 0.15 (3001 hom., cov: 32)
• Consequence: ENSG00000251095 ENST00000506864.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241
• Publications: 0 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506864.5. 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	ENST00000506864.5	TSL:4	n.472-11665G>A		intron	N/A
	ENSG00000251095	ENST00000507916.6	TSL:3	n.135-11665G>A		intron	N/A
	ENSG00000251095	ENST00000508021.5	TSL:4	n.327-11665G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23141 AN: 152012 Hom.: 2989 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0779

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.0553

Gnomad SAS AF: 0.0888

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.152 AC: 23181 AN: 152130 Hom.: 3001 Cov.: 32 AF XY: 0.151 AC XY: 11228 AN XY: 74398

African (AFR) AF: 0.349 AC: 14479 AN: 41454

American (AMR) AF: 0.0777 AC: 1188 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3470

East Asian (EAS) AF: 0.0556 AC: 288 AN: 5182

South Asian (SAS) AF: 0.0882 AC: 425 AN: 4816

European-Finnish (FIN) AF: 0.102 AC: 1085 AN: 10594

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0745 AC: 5071 AN: 68022

Other (OTH) AF: 0.128 AC: 269 AN: 2106

Alfa AF: 0.133 Hom.: 304

Bravo AF: 0.158

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.51
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs3857046; hg19: chr4-90600771;