chr4-89697375-G-A

Variant names:

• chr4-89697375-G-A
• rs3906628
• ENST00000507916.6:n.255+5970G>A

Variant summary

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

The ENST00000507916.6(ENSG00000251095):​n.255+5970G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 151,694 control chromosomes in the GnomAD database, including 8,695 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 0.26 (8695 hom., cov: 32)
• Consequence: ENSG00000251095 ENST00000507916.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 3 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900602	XR_007058466.1	n.9901+5970G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251095	ENST00000507916.6	n.255+5970G>A		intron_variant	Intron 2 of 2	3
ENSG00000251095	ENST00000508021.5	n.447+5970G>A		intron_variant	Intron 4 of 4	4
ENSG00000251095	ENST00000659878.1	n.480-29009G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38863 AN: 151572 Hom.: 8671 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.257 AC: 38933 AN: 151694 Hom.: 8695 Cov.: 32 AF XY: 0.252 AC XY: 18649 AN XY: 74138

African (AFR) AF: 0.612 AC: 25310 AN: 41388

American (AMR) AF: 0.135 AC: 2052 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 632 AN: 3470

East Asian (EAS) AF: 0.0682 AC: 347 AN: 5090

South Asian (SAS) AF: 0.102 AC: 488 AN: 4800

European-Finnish (FIN) AF: 0.125 AC: 1316 AN: 10534

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8158 AN: 67850

Other (OTH) AF: 0.231 AC: 488 AN: 2112

Alfa AF: 0.139 Hom.: 2373

Bravo AF: 0.271

Asia WGS AF: 0.129 AC: 447 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.29
PhyloP100		-0.044

Splicing

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

Other links and lift over

dbSNP: rs3906628; hg19: chr4-90618526;