rs3906628

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-89697375-G-A
• chr4-89697375-G-C

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:53614):

ENSG00000288563 (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.

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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251095	ENST00000507916.6	TSL:3	n.255+5970G>A		intron	N/A
	ENSG00000251095	ENST00000508021.5	TSL:4	n.447+5970G>A		intron	N/A
	ENSG00000251095	ENST00000659878.1		n.480-29009G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3906628;

hg19: chr4-90618526;